Name: rs1253574957
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.

rs1253574957

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:66525364-66525370 (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)₄ / dupA
Variation Type: Indel Insertion and Deletion
Frequency: dupA=0.000038 (10/264690, TOPMED)
del(A)₄=0.00000 (0/14050, ALFA)
dupA=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZDHHC24 : Intron Variant
BBS1 : 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	HWEP
Total	Global	14050	AAAAAAA=1.00000	AAA=0.00000, AAAAAAAA=0.00000	1.0	N/A
European	Sub	9690	AAAAAAA=1.0000	AAA=0.0000, AAAAAAAA=0.0000	1.0	N/A
African	Sub	2898	AAAAAAA=1.0000	AAA=0.0000, AAAAAAAA=0.0000	1.0	N/A
African Others	Sub	114	AAAAAAA=1.000	AAA=0.000, AAAAAAAA=0.000	1.0	N/A
African American	Sub	2784	AAAAAAA=1.0000	AAA=0.0000, AAAAAAAA=0.0000	1.0	N/A
Asian	Sub	112	AAAAAAA=1.000	AAA=0.000, AAAAAAAA=0.000	1.0	N/A
East Asian	Sub	86	AAAAAAA=1.00	AAA=0.00, AAAAAAAA=0.00	1.0	N/A
Other Asian	Sub	26	AAAAAAA=1.00	AAA=0.00, AAAAAAAA=0.00	1.0	N/A
Latin American 1	Sub	146	AAAAAAA=1.000	AAA=0.000, AAAAAAAA=0.000	1.0	N/A
Latin American 2	Sub	610	AAAAAAA=1.000	AAA=0.000, AAAAAAAA=0.000	1.0	N/A
South Asian	Sub	98	AAAAAAA=1.00	AAA=0.00, AAAAAAAA=0.00	1.0	N/A
Other	Sub	496	AAAAAAA=1.000	AAA=0.000, AAAAAAAA=0.000	1.0	N/A

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
TopMed	Global	Study-wide	264690	- No frequency provided	dupA=0.000038
Allele Frequency Aggregator	Total	Global	14050	(A)₇=1.00000	del(A)₄=0.00000, dupA=0.00000
Allele Frequency Aggregator	European	Sub	9690	(A)₇=1.0000	del(A)₄=0.0000, dupA=0.0000
Allele Frequency Aggregator	African	Sub	2898	(A)₇=1.0000	del(A)₄=0.0000, dupA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(A)₇=1.000	del(A)₄=0.000, dupA=0.000
Allele Frequency Aggregator	Other	Sub	496	(A)₇=1.000	del(A)₄=0.000, dupA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(A)₇=1.000	del(A)₄=0.000, dupA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(A)₇=1.000	del(A)₄=0.000, dupA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(A)₇=1.00	del(A)₄=0.00, dupA=0.00

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 11	NC_000011.10:g.66525367_66525370del
GRCh38.p14 chr 11	NC_000011.10:g.66525370dup
GRCh37.p13 chr 11	NC_000011.9:g.66292838_66292841del
GRCh37.p13 chr 11	NC_000011.9:g.66292841dup
BBS1 RefSeqGene	NG_009093.1:g.19720_19723del
BBS1 RefSeqGene	NG_009093.1:g.19723dup

Gene: ZDHHC24, zinc finger DHHC-type containing 24 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZDHHC24 transcript variant 2	NM_001348571.2:c.21+1569… NM_001348571.2:c.21+1569_*21+1572del	N/A	Intron Variant
ZDHHC24 transcript variant 1	NM_207340.3:c.	N/A	Genic Downstream Transcript Variant
ZDHHC24 transcript variant X6	XM_005273874.5:c.21+1569… XM_005273874.5:c.21+1569_*21+1572del	N/A	Intron Variant
ZDHHC24 transcript variant X8	XM_047426710.1:c.560-1091… XM_047426710.1:c.560-1091_560-1088del	N/A	Intron Variant
ZDHHC24 transcript variant X4	XM_011544893.4:c.	N/A	Genic Downstream Transcript Variant
ZDHHC24 transcript variant X7	XM_011544894.3:c.	N/A	Genic Downstream Transcript Variant
ZDHHC24 transcript variant X2	XM_047426709.1:c.	N/A	Genic Downstream Transcript Variant
ZDHHC24 transcript variant X1	XR_007062470.1:n.	N/A	Intron Variant
ZDHHC24 transcript variant X3	XR_007062471.1:n.	N/A	Intron Variant
ZDHHC24 transcript variant X5	XR_949860.4:n.	N/A	Intron Variant

Gene: BBS1, Bardet-Biedl syndrome 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BBS1 transcript	NM_024649.5:c.1111-756_11… NM_024649.5:c.1111-756_1111-753del	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)₇=	del(A)₄	dupA
GRCh38.p14 chr 11	NC_000011.10:g.66525364_66525370=	NC_000011.10:g.66525367_66525370del	NC_000011.10:g.66525370dup
GRCh37.p13 chr 11	NC_000011.9:g.66292835_66292841=	NC_000011.9:g.66292838_66292841del	NC_000011.9:g.66292841dup
BBS1 RefSeqGene	NG_009093.1:g.19717_19723=	NG_009093.1:g.19720_19723del	NG_009093.1:g.19723dup
ZDHHC24 transcript variant 2	NM_001348571.2:c.*21+1572=	NM_001348571.2:c.21+1569_21+1572del	NM_001348571.2:c.*21+1572dup
BBS1 transcript	NM_024649.4:c.1111-759=	NM_024649.4:c.1111-756_1111-753del	NM_024649.4:c.1111-753dup
BBS1 transcript	NM_024649.5:c.1111-759=	NM_024649.5:c.1111-756_1111-753del	NM_024649.5:c.1111-753dup
ZDHHC24 transcript variant X3	XM_005273874.1:c.*21+1572=	XM_005273874.1:c.21+1569_21+1572del	XM_005273874.1:c.*21+1572dup
ZDHHC24 transcript variant X6	XM_005273874.5:c.*21+1572=	XM_005273874.5:c.21+1569_21+1572del	XM_005273874.5:c.*21+1572dup
BBS1 transcript variant X1	XM_005274126.1:c.883-759=	XM_005274126.1:c.883-756_883-753del	XM_005274126.1:c.883-753dup
BBS1 transcript variant X2	XM_005274127.1:c.820-759=	XM_005274127.1:c.820-756_820-753del	XM_005274127.1:c.820-753dup
BBS1 transcript variant X3	XM_005274128.1:c.724-759=	XM_005274128.1:c.724-756_724-753del	XM_005274128.1:c.724-753dup
BBS1 transcript variant X4	XM_005274129.1:c.724-759=	XM_005274129.1:c.724-756_724-753del	XM_005274129.1:c.724-753dup
ZDHHC24 transcript variant X8	XM_047426710.1:c.560-1088=	XM_047426710.1:c.560-1091_560-1088del	XM_047426710.1:c.560-1088dup

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#.

3 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4236755725	Apr 26, 2021 (155)
2	GNOMAD	ss4236755726	Apr 26, 2021 (155)
3	TOPMED	ss4888610784	Apr 26, 2021 (155)
4	gnomAD - Genomes Submission ignored due to conflicting rows: Row 382543202 (NC_000011.10:66525363::A 4/138868) Row 382543203 (NC_000011.10:66525363:AAAA: 1/138868)	-	Apr 26, 2021 (155)
5	gnomAD - Genomes Submission ignored due to conflicting rows: Row 382543202 (NC_000011.10:66525363::A 4/138868) Row 382543203 (NC_000011.10:66525363:AAAA: 1/138868)	-	Apr 26, 2021 (155)
6	TopMed	NC_000011.10 - 66525364	Apr 26, 2021 (155)
7	ALFA	NC_000011.10 - 66525364	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
ss4236755726	NC_000011.10:66525363:AAAA:	NC_000011.10:66525363:AAAAAAA:AAA	(self)
10822575095	NC_000011.10:66525363:AAAAAAA:AAA	NC_000011.10:66525363:AAAAAAA:AAA	(self)
104156440, ss4236755725, ss4888610784	NC_000011.10:66525363::A	NC_000011.10:66525363:AAAAAAA:AAAA… NC_000011.10:66525363:AAAAAAA:AAAAAAAA	(self)
10822575095	NC_000011.10:66525363:AAAAAAA:AAAA… NC_000011.10:66525363:AAAAAAA:AAAAAAAA	NC_000011.10:66525363:AAAAAAA:AAAA… NC_000011.10:66525363:AAAAAAA:AAAAAAAA	(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 rs1253574957

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

rs1253574957