Name: rs59146279
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs59146279

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:149144215-149144233 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: del(A)₈ / del(A)₇ / del(A)₆ / del(…
del(A)₈ / del(A)₇ / del(A)₆ / del(A)₅ / del(A)₄ / delAAA / delAA / delA / dupA / dupAA / dupAAA / dup(A)₅
Variation Type: Indel Insertion and Deletion
Frequency: dupA=0.2219 (1761/7936, ALFA)
del(A)₄=0.0366 (141/3854, ALSPAC)
del(A)₄=0.0388 (144/3708, TWINSUK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HPS3 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	7936	AAAAAAAAAAAAAAAAAAA=0.7576	AAAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000, AAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAA=0.0203, AAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAA=0.0003, AAAAAAAAAAAAAAAAAAAA=0.2219, AAAAAAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAAAAAAAA=0.0000	0.686794	0.134156	0.17905	32
European	Sub	6820	AAAAAAAAAAAAAAAAAAA=0.7182	AAAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000, AAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAA=0.0236, AAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAA=0.0003, AAAAAAAAAAAAAAAAAAAA=0.2579, AAAAAAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAAAAAAAA=0.0000	0.633651	0.157182	0.209166	32
African	Sub	684	AAAAAAAAAAAAAAAAAAA=1.000	AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAAAA=0.000	1.0	0.0	0.0	N/A
African Others	Sub	18	AAAAAAAAAAAAAAAAAAA=1.00	AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAAAA=0.00	1.0	0.0	0.0	N/A
African American	Sub	666	AAAAAAAAAAAAAAAAAAA=1.000	AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAAAA=0.000	1.0	0.0	0.0	N/A
Asian	Sub	34	AAAAAAAAAAAAAAAAAAA=1.00	AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAAAA=0.00	1.0	0.0	0.0	N/A
East Asian	Sub	30	AAAAAAAAAAAAAAAAAAA=1.00	AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAAAA=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	4	AAAAAAAAAAAAAAAAAAA=1.0	AAAAAAAAAAA=0.0, AAAAAAAAAAAA=0.0, AAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAAAAAAAAA=0.0, AAAAAAAAAAAAAAAAAAAAAAAA=0.0	1.0	0.0	0.0	N/A
Latin American 1	Sub	48	AAAAAAAAAAAAAAAAAAA=1.00	AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAAAA=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	198	AAAAAAAAAAAAAAAAAAA=1.000	AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAAAA=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	18	AAAAAAAAAAAAAAAAAAA=1.00	AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAAAAAAAA=0.00	1.0	0.0	0.0	N/A
Other	Sub	134	AAAAAAAAAAAAAAAAAAA=0.985	AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAA=0.015, AAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAAAAAAAA=0.000	0.970149	0.0	0.029851	0

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	7936	(A)₁₉=0.7576	del(A)₈=0.0000, del(A)₇=0.0000, del(A)₆=0.0000, del(A)₅=0.0000, del(A)₄=0.0203, delAAA=0.0000, delAA=0.0000, delA=0.0003, dupA=0.2219, dupAA=0.0000, dupAAA=0.0000, dup(A)₅=0.0000
Allele Frequency Aggregator	European	Sub	6820	(A)₁₉=0.7182	del(A)₈=0.0000, del(A)₇=0.0000, del(A)₆=0.0000, del(A)₅=0.0000, del(A)₄=0.0236, delAAA=0.0000, delAA=0.0000, delA=0.0003, dupA=0.2579, dupAA=0.0000, dupAAA=0.0000, dup(A)₅=0.0000
Allele Frequency Aggregator	African	Sub	684	(A)₁₉=1.000	del(A)₈=0.000, del(A)₇=0.000, del(A)₆=0.000, del(A)₅=0.000, del(A)₄=0.000, delAAA=0.000, delAA=0.000, delA=0.000, dupA=0.000, dupAA=0.000, dupAAA=0.000, dup(A)₅=0.000
Allele Frequency Aggregator	Latin American 2	Sub	198	(A)₁₉=1.000	del(A)₈=0.000, del(A)₇=0.000, del(A)₆=0.000, del(A)₅=0.000, del(A)₄=0.000, delAAA=0.000, delAA=0.000, delA=0.000, dupA=0.000, dupAA=0.000, dupAAA=0.000, dup(A)₅=0.000
Allele Frequency Aggregator	Other	Sub	134	(A)₁₉=0.985	del(A)₈=0.000, del(A)₇=0.000, del(A)₆=0.000, del(A)₅=0.000, del(A)₄=0.000, delAAA=0.000, delAA=0.000, delA=0.000, dupA=0.015, dupAA=0.000, dupAAA=0.000, dup(A)₅=0.000
Allele Frequency Aggregator	Latin American 1	Sub	48	(A)₁₉=1.00	del(A)₈=0.00, del(A)₇=0.00, del(A)₆=0.00, del(A)₅=0.00, del(A)₄=0.00, delAAA=0.00, delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00, dupAAA=0.00, dup(A)₅=0.00
Allele Frequency Aggregator	Asian	Sub	34	(A)₁₉=1.00	del(A)₈=0.00, del(A)₇=0.00, del(A)₆=0.00, del(A)₅=0.00, del(A)₄=0.00, delAAA=0.00, delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00, dupAAA=0.00, dup(A)₅=0.00
Allele Frequency Aggregator	South Asian	Sub	18	(A)₁₉=1.00	del(A)₈=0.00, del(A)₇=0.00, del(A)₆=0.00, del(A)₅=0.00, del(A)₄=0.00, delAAA=0.00, delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00, dupAAA=0.00, dup(A)₅=0.00
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	(A)₁₉=0.9634	del(A)₄=0.0366
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	(A)₁₉=0.9612	del(A)₄=0.0388

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 3	NC_000003.12:g.149144226_149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144227_149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144228_149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144229_149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144230_149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144231_149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144232_149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144233del
GRCh38.p14 chr 3	NC_000003.12:g.149144233dup
GRCh38.p14 chr 3	NC_000003.12:g.149144232_149144233dup
GRCh38.p14 chr 3	NC_000003.12:g.149144231_149144233dup
GRCh38.p14 chr 3	NC_000003.12:g.149144229_149144233dup
GRCh37.p13 chr 3	NC_000003.11:g.148862013_148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862014_148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862015_148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862016_148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862017_148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862018_148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862019_148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862020del
GRCh37.p13 chr 3	NC_000003.11:g.148862020dup
GRCh37.p13 chr 3	NC_000003.11:g.148862019_148862020dup
GRCh37.p13 chr 3	NC_000003.11:g.148862018_148862020dup
GRCh37.p13 chr 3	NC_000003.11:g.148862016_148862020dup
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19643_19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19644_19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19645_19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19646_19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19647_19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19648_19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19649_19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19650del
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19650dup
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19649_19650dup
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19648_19650dup
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19646_19650dup

Gene: HPS3, HPS3 biogenesis of lysosomal organelles complex 2 subunit 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HPS3 transcript variant 2	NM_001308258.2:c.476-1128… NM_001308258.2:c.476-1128_476-1121del	N/A	Intron Variant
HPS3 transcript variant 1	NM_032383.5:c.971-1128_97… NM_032383.5:c.971-1128_971-1121del	N/A	Intron Variant
HPS3 transcript variant X3	XM_005247834.5:c.971-1128… XM_005247834.5:c.971-1128_971-1121del	N/A	Intron Variant
HPS3 transcript variant X1	XM_047449064.1:c.971-1128… XM_047449064.1:c.971-1128_971-1121del	N/A	Intron Variant
HPS3 transcript variant X2	XR_001740328.3:n.	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	(A)₁₉=	del(A)₈	del(A)₇	del(A)₆	del(A)₅	del(A)₄	delAAA	delAA	delA	dupA	dupAA	dupAAA	dup(A)₅
GRCh38.p14 chr 3	NC_000003.12:g.149144215_149144233=	NC_000003.12:g.149144226_149144233del	NC_000003.12:g.149144227_149144233del	NC_000003.12:g.149144228_149144233del	NC_000003.12:g.149144229_149144233del	NC_000003.12:g.149144230_149144233del	NC_000003.12:g.149144231_149144233del	NC_000003.12:g.149144232_149144233del	NC_000003.12:g.149144233del	NC_000003.12:g.149144233dup	NC_000003.12:g.149144232_149144233dup	NC_000003.12:g.149144231_149144233dup	NC_000003.12:g.149144229_149144233dup
GRCh37.p13 chr 3	NC_000003.11:g.148862002_148862020=	NC_000003.11:g.148862013_148862020del	NC_000003.11:g.148862014_148862020del	NC_000003.11:g.148862015_148862020del	NC_000003.11:g.148862016_148862020del	NC_000003.11:g.148862017_148862020del	NC_000003.11:g.148862018_148862020del	NC_000003.11:g.148862019_148862020del	NC_000003.11:g.148862020del	NC_000003.11:g.148862020dup	NC_000003.11:g.148862019_148862020dup	NC_000003.11:g.148862018_148862020dup	NC_000003.11:g.148862016_148862020dup
HPS3 RefSeqGene (LRG_563)	NG_009847.1:g.19632_19650=	NG_009847.1:g.19643_19650del	NG_009847.1:g.19644_19650del	NG_009847.1:g.19645_19650del	NG_009847.1:g.19646_19650del	NG_009847.1:g.19647_19650del	NG_009847.1:g.19648_19650del	NG_009847.1:g.19649_19650del	NG_009847.1:g.19650del	NG_009847.1:g.19650dup	NG_009847.1:g.19649_19650dup	NG_009847.1:g.19648_19650dup	NG_009847.1:g.19646_19650dup
HPS3 transcript variant 2	NM_001308258.2:c.476-1139=	NM_001308258.2:c.476-1128_476-1121del	NM_001308258.2:c.476-1127_476-1121del	NM_001308258.2:c.476-1126_476-1121del	NM_001308258.2:c.476-1125_476-1121del	NM_001308258.2:c.476-1124_476-1121del	NM_001308258.2:c.476-1123_476-1121del	NM_001308258.2:c.476-1122_476-1121del	NM_001308258.2:c.476-1121del	NM_001308258.2:c.476-1121dup	NM_001308258.2:c.476-1122_476-1121dup	NM_001308258.2:c.476-1123_476-1121dup	NM_001308258.2:c.476-1125_476-1121dup
HPS3 transcript	NM_032383.3:c.971-1139=	NM_032383.3:c.971-1128_971-1121del	NM_032383.3:c.971-1127_971-1121del	NM_032383.3:c.971-1126_971-1121del	NM_032383.3:c.971-1125_971-1121del	NM_032383.3:c.971-1124_971-1121del	NM_032383.3:c.971-1123_971-1121del	NM_032383.3:c.971-1122_971-1121del	NM_032383.3:c.971-1121del	NM_032383.3:c.971-1121dup	NM_032383.3:c.971-1122_971-1121dup	NM_032383.3:c.971-1123_971-1121dup	NM_032383.3:c.971-1125_971-1121dup
HPS3 transcript variant 1	NM_032383.5:c.971-1139=	NM_032383.5:c.971-1128_971-1121del	NM_032383.5:c.971-1127_971-1121del	NM_032383.5:c.971-1126_971-1121del	NM_032383.5:c.971-1125_971-1121del	NM_032383.5:c.971-1124_971-1121del	NM_032383.5:c.971-1123_971-1121del	NM_032383.5:c.971-1122_971-1121del	NM_032383.5:c.971-1121del	NM_032383.5:c.971-1121dup	NM_032383.5:c.971-1122_971-1121dup	NM_032383.5:c.971-1123_971-1121dup	NM_032383.5:c.971-1125_971-1121dup
HPS3 transcript variant X1	XM_005247833.1:c.476-1139=	XM_005247833.1:c.476-1128_476-1121del	XM_005247833.1:c.476-1127_476-1121del	XM_005247833.1:c.476-1126_476-1121del	XM_005247833.1:c.476-1125_476-1121del	XM_005247833.1:c.476-1124_476-1121del	XM_005247833.1:c.476-1123_476-1121del	XM_005247833.1:c.476-1122_476-1121del	XM_005247833.1:c.476-1121del	XM_005247833.1:c.476-1121dup	XM_005247833.1:c.476-1122_476-1121dup	XM_005247833.1:c.476-1123_476-1121dup	XM_005247833.1:c.476-1125_476-1121dup
HPS3 transcript variant X2	XM_005247834.1:c.971-1139=	XM_005247834.1:c.971-1128_971-1121del	XM_005247834.1:c.971-1127_971-1121del	XM_005247834.1:c.971-1126_971-1121del	XM_005247834.1:c.971-1125_971-1121del	XM_005247834.1:c.971-1124_971-1121del	XM_005247834.1:c.971-1123_971-1121del	XM_005247834.1:c.971-1122_971-1121del	XM_005247834.1:c.971-1121del	XM_005247834.1:c.971-1121dup	XM_005247834.1:c.971-1122_971-1121dup	XM_005247834.1:c.971-1123_971-1121dup	XM_005247834.1:c.971-1125_971-1121dup
HPS3 transcript variant X3	XM_005247834.5:c.971-1139=	XM_005247834.5:c.971-1128_971-1121del	XM_005247834.5:c.971-1127_971-1121del	XM_005247834.5:c.971-1126_971-1121del	XM_005247834.5:c.971-1125_971-1121del	XM_005247834.5:c.971-1124_971-1121del	XM_005247834.5:c.971-1123_971-1121del	XM_005247834.5:c.971-1122_971-1121del	XM_005247834.5:c.971-1121del	XM_005247834.5:c.971-1121dup	XM_005247834.5:c.971-1122_971-1121dup	XM_005247834.5:c.971-1123_971-1121dup	XM_005247834.5:c.971-1125_971-1121dup
HPS3 transcript variant X1	XM_047449064.1:c.971-1139=	XM_047449064.1:c.971-1128_971-1121del	XM_047449064.1:c.971-1127_971-1121del	XM_047449064.1:c.971-1126_971-1121del	XM_047449064.1:c.971-1125_971-1121del	XM_047449064.1:c.971-1124_971-1121del	XM_047449064.1:c.971-1123_971-1121del	XM_047449064.1:c.971-1122_971-1121del	XM_047449064.1:c.971-1121del	XM_047449064.1:c.971-1121dup	XM_047449064.1:c.971-1122_971-1121dup	XM_047449064.1:c.971-1123_971-1121dup	XM_047449064.1:c.971-1125_971-1121dup

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

46 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss81649746	Dec 15, 2007 (129)
2	SSMP	ss663365742	Apr 01, 2015 (144)
3	BILGI_BIOE	ss666230868	Apr 25, 2013 (138)
4	EVA_UK10K_ALSPAC	ss1703872036	Apr 01, 2015 (144)
5	EVA_UK10K_TWINSUK	ss1703872538	Apr 01, 2015 (144)
6	SWEGEN	ss2993395645	Nov 08, 2017 (151)
7	URBANLAB	ss3647553884	Oct 12, 2018 (152)
8	EVA_DECODE	ss3710531152	Jul 13, 2019 (153)
9	EVA_DECODE	ss3710531153	Jul 13, 2019 (153)
10	EVA_DECODE	ss3710531154	Jul 13, 2019 (153)
11	EVA_DECODE	ss3710531155	Jul 13, 2019 (153)
12	EVA_DECODE	ss3710531156	Jul 13, 2019 (153)
13	EVA_DECODE	ss3710531157	Jul 13, 2019 (153)
14	EVA	ss3828136022	Apr 25, 2020 (154)
15	GNOMAD	ss4082980819	Apr 26, 2021 (155)
16	GNOMAD	ss4082980820	Apr 26, 2021 (155)
17	GNOMAD	ss4082980821	Apr 26, 2021 (155)
18	GNOMAD	ss4082980822	Apr 26, 2021 (155)
19	GNOMAD	ss4082980823	Apr 26, 2021 (155)
20	GNOMAD	ss4082980824	Apr 26, 2021 (155)
21	GNOMAD	ss4082980825	Apr 26, 2021 (155)
22	GNOMAD	ss4082980826	Apr 26, 2021 (155)
23	GNOMAD	ss4082980827	Apr 26, 2021 (155)
24	TOMMO_GENOMICS	ss5162144751	Apr 26, 2021 (155)
25	TOMMO_GENOMICS	ss5162144752	Apr 26, 2021 (155)
26	TOMMO_GENOMICS	ss5162144753	Apr 26, 2021 (155)
27	TOMMO_GENOMICS	ss5162144754	Apr 26, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5256462200	Oct 12, 2022 (156)
29	1000G_HIGH_COVERAGE	ss5256462201	Oct 12, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5256462202	Oct 12, 2022 (156)
31	1000G_HIGH_COVERAGE	ss5256462203	Oct 12, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5256462204	Oct 12, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5256462205	Oct 12, 2022 (156)
34	HUGCELL_USP	ss5455557428	Oct 12, 2022 (156)
35	HUGCELL_USP	ss5455557429	Oct 12, 2022 (156)
36	HUGCELL_USP	ss5455557430	Oct 12, 2022 (156)
37	HUGCELL_USP	ss5455557431	Oct 12, 2022 (156)
38	HUGCELL_USP	ss5455557432	Oct 12, 2022 (156)
39	TOMMO_GENOMICS	ss5695185518	Oct 12, 2022 (156)
40	TOMMO_GENOMICS	ss5695185519	Oct 12, 2022 (156)
41	TOMMO_GENOMICS	ss5695185520	Oct 12, 2022 (156)
42	TOMMO_GENOMICS	ss5695185522	Oct 12, 2022 (156)
43	EVA	ss5826647146	Oct 12, 2022 (156)
44	EVA	ss5853889558	Oct 12, 2022 (156)
45	EVA	ss5871503833	Oct 12, 2022 (156)
46	EVA	ss5961798321	Oct 12, 2022 (156)
47	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 148862002	Oct 12, 2018 (152)
48	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
49	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
50	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
51	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
52	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
53	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
54	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
55	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
56	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
57	gnomAD - Genomes Submission ignored due to conflicting rows: Row 127446452 (NC_000003.12:149144214::A 45632/113358) Row 127446453 (NC_000003.12:149144214::AA 2891/113548) Row 127446454 (NC_000003.12:149144214::AAA 3/113584)...	-	Apr 26, 2021 (155)
58	8.3KJPN Submission ignored due to conflicting rows: Row 20114058 (NC_000003.11:148862001::A 6490/16752) Row 20114059 (NC_000003.11:148862001::AA 12/16752) Row 20114060 (NC_000003.11:148862001:A: 65/16752)...	-	Apr 26, 2021 (155)
59	8.3KJPN Submission ignored due to conflicting rows: Row 20114058 (NC_000003.11:148862001::A 6490/16752) Row 20114059 (NC_000003.11:148862001::AA 12/16752) Row 20114060 (NC_000003.11:148862001:A: 65/16752)...	-	Apr 26, 2021 (155)
60	8.3KJPN Submission ignored due to conflicting rows: Row 20114058 (NC_000003.11:148862001::A 6490/16752) Row 20114059 (NC_000003.11:148862001::AA 12/16752) Row 20114060 (NC_000003.11:148862001:A: 65/16752)...	-	Apr 26, 2021 (155)
61	8.3KJPN Submission ignored due to conflicting rows: Row 20114058 (NC_000003.11:148862001::A 6490/16752) Row 20114059 (NC_000003.11:148862001::AA 12/16752) Row 20114060 (NC_000003.11:148862001:A: 65/16752)...	-	Apr 26, 2021 (155)
62	14KJPN Submission ignored due to conflicting rows: Row 29022622 (NC_000003.12:149144214::A 10661/28214) Row 29022623 (NC_000003.12:149144214::AA 12/28214) Row 29022624 (NC_000003.12:149144214:A: 113/28214)...	-	Oct 12, 2022 (156)
63	14KJPN Submission ignored due to conflicting rows: Row 29022622 (NC_000003.12:149144214::A 10661/28214) Row 29022623 (NC_000003.12:149144214::AA 12/28214) Row 29022624 (NC_000003.12:149144214:A: 113/28214)...	-	Oct 12, 2022 (156)
64	14KJPN Submission ignored due to conflicting rows: Row 29022622 (NC_000003.12:149144214::A 10661/28214) Row 29022623 (NC_000003.12:149144214::AA 12/28214) Row 29022624 (NC_000003.12:149144214:A: 113/28214)...	-	Oct 12, 2022 (156)
65	14KJPN Submission ignored due to conflicting rows: Row 29022622 (NC_000003.12:149144214::A 10661/28214) Row 29022623 (NC_000003.12:149144214::AA 12/28214) Row 29022624 (NC_000003.12:149144214:A: 113/28214)...	-	Oct 12, 2022 (156)
66	UK 10K study - Twins	NC_000003.11 - 148862002	Oct 12, 2018 (152)
67	ALFA	NC_000003.12 - 149144215	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAA	(self)
ss4082980827	NC_000003.12:149144214:AAAAAAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAA	(self)
ss5162144754	NC_000003.11:148862001:AAAAAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAA	(self)
ss4082980826, ss5695185522	NC_000003.12:149144214:AAAAAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAA	(self)
ss3710531157, ss4082980825, ss5256462202, ss5455557432, ss5871503833	NC_000003.12:149144214:AAAAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA	(self)
9990908, 9990908, ss666230868, ss1703872036, ss1703872538, ss2993395645, ss5826647146, ss5961798321	NC_000003.11:148862001:AAAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA	(self)
ss3647553884, ss4082980824, ss5256462203, ss5455557431	NC_000003.12:149144214:AAAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA	(self)
ss3710531156	NC_000003.12:149144215:AAAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA	(self)
ss3828136022	NC_000003.11:148862001:AAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA	(self)
ss4082980823	NC_000003.12:149144214:AAA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA	(self)
ss4082980822	NC_000003.12:149144214:AA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA	(self)
ss3710531155	NC_000003.12:149144217:AA:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA	(self)
ss5162144753	NC_000003.11:148862001:A:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA	(self)
ss5256462204, ss5455557430, ss5695185520	NC_000003.12:149144214:A:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA	(self)
ss3710531154	NC_000003.12:149144218:A:	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA	(self)
ss663365742, ss5162144751	NC_000003.11:148862001::A	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA	(self)
ss4082980819, ss5256462200, ss5455557428, ss5695185518, ss5853889558	NC_000003.12:149144214::A	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA	(self)
ss3710531153	NC_000003.12:149144219::A	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA	(self)
ss81649746	NT_005612.16:55357166::A	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA	(self)
ss5162144752	NC_000003.11:148862001::AA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA	(self)
ss4082980820, ss5256462201, ss5455557429, ss5695185519	NC_000003.12:149144214::AA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA	(self)
ss3710531152	NC_000003.12:149144219::AA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA	(self)
ss4082980821, ss5256462205	NC_000003.12:149144214::AAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAA	(self)
1887861362	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAA	NC_000003.12:149144214:AAAAAAAAAAA… NC_000003.12:149144214:AAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAA	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs59146279

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs59146279