Name: rs1491380005
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.

rs1491380005

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:3814775-3814777 (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: delCT
Variation Type: Indel Insertion and Deletion
Frequency: delCT=0.00013 (13/96500, GnomAD)
delCT=0.00019 (3/16198, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PGAP2 : Intron Variant
LOC124902618 : 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	HTRZ	HWEP
Total	Global	16198	TCT=0.99981	T=0.00019	0.99963	0.00037	0
European	Sub	11946	TCT=0.99975	T=0.00025	0.999498	0.000502	0
African	Sub	2816	TCT=1.0000	T=0.0000	1.0	0.0	N/A
African Others	Sub	108	TCT=1.000	T=0.000	1.0	0.0	N/A
African American	Sub	2708	TCT=1.0000	T=0.0000	1.0	0.0	N/A
Asian	Sub	108	TCT=1.000	T=0.000	1.0	0.0	N/A
East Asian	Sub	84	TCT=1.00	T=0.00	1.0	0.0	N/A
Other Asian	Sub	24	TCT=1.00	T=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	TCT=1.000	T=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	TCT=1.000	T=0.000	1.0	0.0	N/A
South Asian	Sub	94	TCT=1.00	T=0.00	1.0	0.0	N/A
Other	Sub	478	TCT=1.000	T=0.000	1.0	0.0	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
gnomAD - Genomes	Global	Study-wide	96500	TCT=0.99987	delCT=0.00013
gnomAD - Genomes	European	Sub	45808	TCT=0.99980	delCT=0.00020
gnomAD - Genomes	African	Sub	35664	TCT=1.00000	delCT=0.00000
gnomAD - Genomes	American	Sub	8864	TCT=0.9999	delCT=0.0001
gnomAD - Genomes	Ashkenazi Jewish	Sub	2566	TCT=0.9992	delCT=0.0008
gnomAD - Genomes	East Asian	Sub	2108	TCT=1.0000	delCT=0.0000
gnomAD - Genomes	Other	Sub	1490	TCT=0.9993	delCT=0.0007
Allele Frequency Aggregator	Total	Global	16198	TCT=0.99981	delCT=0.00019
Allele Frequency Aggregator	European	Sub	11946	TCT=0.99975	delCT=0.00025
Allele Frequency Aggregator	African	Sub	2816	TCT=1.0000	delCT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	TCT=1.000	delCT=0.000
Allele Frequency Aggregator	Other	Sub	478	TCT=1.000	delCT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	TCT=1.000	delCT=0.000
Allele Frequency Aggregator	Asian	Sub	108	TCT=1.000	delCT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	TCT=1.00	delCT=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.3814776_3814777del
GRCh37.p13 chr 11	NC_000011.9:g.3836006_3836007del
PGAP2 RefSeqGene	NG_051812.1:g.22053_22054del

Gene: PGAP2, post-GPI attachment to proteins 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PGAP2 transcript variant 2	NM_001145438.2:c.336+3352… NM_001145438.2:c.336+3352_336+3353del	N/A	Intron Variant
PGAP2 transcript variant 4	NM_001256235.1:c.134+3352… NM_001256235.1:c.134+3352_134+3353del	N/A	Intron Variant
PGAP2 transcript variant 5	NM_001256236.1:c.337-2577… NM_001256236.1:c.337-2577_337-2576del	N/A	Intron Variant
PGAP2 transcript variant 9	NM_001256237.1:c.336+3352… NM_001256237.1:c.336+3352_336+3353del	N/A	Intron Variant
PGAP2 transcript variant 10	NM_001256238.1:c.165+3352… NM_001256238.1:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant 11	NM_001256239.2:c.165+3352… NM_001256239.2:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant 12	NM_001256240.2:c.165+3352… NM_001256240.2:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant 17	NM_001283038.1:c.336+3352… NM_001283038.1:c.336+3352_336+3353del	N/A	Intron Variant
PGAP2 transcript variant 18	NM_001283039.1:c.161+6461… NM_001283039.1:c.161+6461_161+6462del	N/A	Intron Variant
PGAP2 transcript variant 19	NM_001283040.1:c.161+6461… NM_001283040.1:c.161+6461_161+6462del	N/A	Intron Variant
PGAP2 transcript variant 23	NM_001346397.2:c.318+3352… NM_001346397.2:c.318+3352_318+3353del	N/A	Intron Variant
PGAP2 transcript variant 24	NM_001346398.2:c.165+3352… NM_001346398.2:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant 26	NM_001346399.2:c.-39+3352… NM_001346399.2:c.-39+3352_-39+3353del	N/A	Intron Variant
PGAP2 transcript variant 27	NM_001346400.2:c.165+3352… NM_001346400.2:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant 28	NM_001346401.2:c.-39+3352… NM_001346401.2:c.-39+3352_-39+3353del	N/A	Intron Variant
PGAP2 transcript variant 29	NM_001346402.2:c.200+3352… NM_001346402.2:c.200+3352_200+3353del	N/A	Intron Variant
PGAP2 transcript variant 30	NM_001346403.1:c.166-2577… NM_001346403.1:c.166-2577_166-2576del	N/A	Intron Variant
PGAP2 transcript variant 31	NM_001346404.1:c.165+3352… NM_001346404.1:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant 32	NM_001346405.1:c.165+3352… NM_001346405.1:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant 1	NM_014489.4:c.166-2577_16… NM_014489.4:c.166-2577_166-2576del	N/A	Intron Variant
PGAP2 transcript variant 6	NR_027016.3:n.	N/A	Intron Variant
PGAP2 transcript variant 7	NR_027017.4:n.	N/A	Intron Variant
PGAP2 transcript variant 8	NR_027018.2:n.	N/A	Intron Variant
PGAP2 transcript variant 3	NR_045923.2:n.	N/A	Intron Variant
PGAP2 transcript variant 13	NR_045925.2:n.	N/A	Intron Variant
PGAP2 transcript variant 14	NR_045926.2:n.	N/A	Intron Variant
PGAP2 transcript variant 15	NR_045927.2:n.	N/A	Intron Variant
PGAP2 transcript variant 16	NR_045929.2:n.	N/A	Intron Variant
PGAP2 transcript variant 20	NR_104270.2:n.	N/A	Intron Variant
PGAP2 transcript variant 21	NR_104271.2:n.	N/A	Intron Variant
PGAP2 transcript variant 22	NR_104272.2:n.	N/A	Intron Variant
PGAP2 transcript variant 25	NR_144427.2:n.	N/A	Intron Variant
PGAP2 transcript variant 33	NR_144428.2:n.	N/A	Intron Variant
PGAP2 transcript variant 34	NR_144429.2:n.	N/A	Intron Variant
PGAP2 transcript variant 35	NR_144430.2:n.	N/A	Intron Variant
PGAP2 transcript variant X16	XM_006718185.3:c.161+6461… XM_006718185.3:c.161+6461_161+6462del	N/A	Intron Variant
PGAP2 transcript variant X1	XM_011519990.3:c.166-2577… XM_011519990.3:c.166-2577_166-2576del	N/A	Intron Variant
PGAP2 transcript variant X2	XM_011519991.3:c.166-2577… XM_011519991.3:c.166-2577_166-2576del	N/A	Intron Variant
PGAP2 transcript variant X3	XM_011519992.2:c.201-2529… XM_011519992.2:c.201-2529_201-2528del	N/A	Intron Variant
PGAP2 transcript variant X8	XM_011519996.2:c.201-2577… XM_011519996.2:c.201-2577_201-2576del	N/A	Intron Variant
PGAP2 transcript variant X9	XM_011519998.3:c.135-2529… XM_011519998.3:c.135-2529_135-2528del	N/A	Intron Variant
PGAP2 transcript variant X10	XM_011519999.2:c.135-2529… XM_011519999.2:c.135-2529_135-2528del	N/A	Intron Variant
PGAP2 transcript variant X12	XM_011520002.2:c.165+3352… XM_011520002.2:c.165+3352_165+3353del	N/A	Intron Variant
PGAP2 transcript variant X14	XM_011520004.3:c.319-2577… XM_011520004.3:c.319-2577_319-2576del	N/A	Intron Variant
PGAP2 transcript variant X18	XM_024448443.2:c.134+3352… XM_024448443.2:c.134+3352_134+3353del	N/A	Intron Variant
PGAP2 transcript variant X19	XM_024448444.2:c.134+3352… XM_024448444.2:c.134+3352_134+3353del	N/A	Intron Variant
PGAP2 transcript variant X4	XM_047426776.1:c.166-2577… XM_047426776.1:c.166-2577_166-2576del	N/A	Intron Variant
PGAP2 transcript variant X5	XM_047426777.1:c.337-2577… XM_047426777.1:c.337-2577_337-2576del	N/A	Intron Variant
PGAP2 transcript variant X6	XM_047426778.1:c.201-2529… XM_047426778.1:c.201-2529_201-2528del	N/A	Intron Variant
PGAP2 transcript variant X7	XM_047426779.1:c.-49-2577… XM_047426779.1:c.-49-2577_-49-2576del	N/A	Intron Variant
PGAP2 transcript variant X11	XM_047426780.1:c.162-2577… XM_047426780.1:c.162-2577_162-2576del	N/A	Intron Variant
PGAP2 transcript variant X15	XM_047426781.1:c.166-2577… XM_047426781.1:c.166-2577_166-2576del	N/A	Intron Variant
PGAP2 transcript variant X17	XM_047426782.1:c.161+6461… XM_047426782.1:c.161+6461_161+6462del	N/A	Intron Variant
PGAP2 transcript variant X20	XM_047426784.1:c.200+3352… XM_047426784.1:c.200+3352_200+3353del	N/A	Intron Variant
PGAP2 transcript variant X21	XM_047426785.1:c.200+3352… XM_047426785.1:c.200+3352_200+3353del	N/A	Intron Variant
PGAP2 transcript variant X22	XM_047426786.1:c.-15-2577… XM_047426786.1:c.-15-2577_-15-2576del	N/A	Intron Variant
PGAP2 transcript variant X23	XM_047426787.1:c.-15-2577… XM_047426787.1:c.-15-2577_-15-2576del	N/A	Intron Variant
PGAP2 transcript variant X24	XM_047426788.1:c.143+6461… XM_047426788.1:c.143+6461_143+6462del	N/A	Intron Variant
PGAP2 transcript variant X25	XM_047426789.1:c.-39+6461… XM_047426789.1:c.-39+6461_-39+6462del	N/A	Intron Variant
PGAP2 transcript variant X26	XM_047426790.1:c.-39+6125… XM_047426790.1:c.-39+6125_-39+6126del	N/A	Intron Variant
PGAP2 transcript variant X27	XM_047426792.1:c.-39+6461… XM_047426792.1:c.-39+6461_-39+6462del	N/A	Intron Variant
PGAP2 transcript variant X28	XM_047426793.1:c.143+6461… XM_047426793.1:c.143+6461_143+6462del	N/A	Intron Variant
PGAP2 transcript variant X13	XM_006718181.4:c.	N/A	Genic Upstream Transcript Variant
PGAP2 transcript variant X29	XM_047426783.1:c.	N/A	Genic Upstream Transcript Variant
PGAP2 transcript variant X30	XM_047426791.1:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC124902618, uncharacterized LOC124902618 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124902618 transcript	XR_007062559.1: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	TCT=	delCT
GRCh38.p14 chr 11	NC_000011.10:g.3814775_3814777=	NC_000011.10:g.3814776_3814777del
GRCh37.p13 chr 11	NC_000011.9:g.3836005_3836007=	NC_000011.9:g.3836006_3836007del
PGAP2 RefSeqGene	NG_051812.1:g.22052_22054=	NG_051812.1:g.22053_22054del
PGAP2 transcript variant 2	NM_001145438.2:c.336+3351=	NM_001145438.2:c.336+3352_336+3353del
PGAP2 transcript variant 4	NM_001256235.1:c.134+3351=	NM_001256235.1:c.134+3352_134+3353del
PGAP2 transcript variant 5	NM_001256236.1:c.337-2578=	NM_001256236.1:c.337-2577_337-2576del
PGAP2 transcript variant 9	NM_001256237.1:c.336+3351=	NM_001256237.1:c.336+3352_336+3353del
PGAP2 transcript variant 10	NM_001256238.1:c.165+3351=	NM_001256238.1:c.165+3352_165+3353del
PGAP2 transcript variant 11	NM_001256239.1:c.165+3351=	NM_001256239.1:c.165+3352_165+3353del
PGAP2 transcript variant 11	NM_001256239.2:c.165+3351=	NM_001256239.2:c.165+3352_165+3353del
PGAP2 transcript variant 12	NM_001256240.1:c.165+3351=	NM_001256240.1:c.165+3352_165+3353del
PGAP2 transcript variant 12	NM_001256240.2:c.165+3351=	NM_001256240.2:c.165+3352_165+3353del
PGAP2 transcript variant 17	NM_001283038.1:c.336+3351=	NM_001283038.1:c.336+3352_336+3353del
PGAP2 transcript variant 18	NM_001283039.1:c.161+6460=	NM_001283039.1:c.161+6461_161+6462del
PGAP2 transcript variant 19	NM_001283040.1:c.161+6460=	NM_001283040.1:c.161+6461_161+6462del
PGAP2 transcript variant 23	NM_001346397.2:c.318+3351=	NM_001346397.2:c.318+3352_318+3353del
PGAP2 transcript variant 24	NM_001346398.2:c.165+3351=	NM_001346398.2:c.165+3352_165+3353del
PGAP2 transcript variant 26	NM_001346399.2:c.-39+3351=	NM_001346399.2:c.-39+3352_-39+3353del
PGAP2 transcript variant 27	NM_001346400.2:c.165+3351=	NM_001346400.2:c.165+3352_165+3353del
PGAP2 transcript variant 28	NM_001346401.2:c.-39+3351=	NM_001346401.2:c.-39+3352_-39+3353del
PGAP2 transcript variant 29	NM_001346402.2:c.200+3351=	NM_001346402.2:c.200+3352_200+3353del
PGAP2 transcript variant 30	NM_001346403.1:c.166-2578=	NM_001346403.1:c.166-2577_166-2576del
PGAP2 transcript variant 31	NM_001346404.1:c.165+3351=	NM_001346404.1:c.165+3352_165+3353del
PGAP2 transcript variant 32	NM_001346405.1:c.165+3351=	NM_001346405.1:c.165+3352_165+3353del
PGAP2 transcript variant 1	NM_014489.3:c.166-2578=	NM_014489.3:c.166-2577_166-2576del
PGAP2 transcript variant 1	NM_014489.4:c.166-2578=	NM_014489.4:c.166-2577_166-2576del
PGAP2 transcript variant X16	XM_006718185.3:c.161+6460=	XM_006718185.3:c.161+6461_161+6462del
PGAP2 transcript variant X1	XM_011519990.3:c.166-2578=	XM_011519990.3:c.166-2577_166-2576del
PGAP2 transcript variant X2	XM_011519991.3:c.166-2578=	XM_011519991.3:c.166-2577_166-2576del
PGAP2 transcript variant X3	XM_011519992.2:c.201-2530=	XM_011519992.2:c.201-2529_201-2528del
PGAP2 transcript variant X8	XM_011519996.2:c.201-2578=	XM_011519996.2:c.201-2577_201-2576del
PGAP2 transcript variant X9	XM_011519998.3:c.135-2530=	XM_011519998.3:c.135-2529_135-2528del
PGAP2 transcript variant X10	XM_011519999.2:c.135-2530=	XM_011519999.2:c.135-2529_135-2528del
PGAP2 transcript variant X12	XM_011520002.2:c.165+3351=	XM_011520002.2:c.165+3352_165+3353del
PGAP2 transcript variant X14	XM_011520004.3:c.319-2578=	XM_011520004.3:c.319-2577_319-2576del
PGAP2 transcript variant X18	XM_024448443.2:c.134+3351=	XM_024448443.2:c.134+3352_134+3353del
PGAP2 transcript variant X19	XM_024448444.2:c.134+3351=	XM_024448444.2:c.134+3352_134+3353del
PGAP2 transcript variant X4	XM_047426776.1:c.166-2578=	XM_047426776.1:c.166-2577_166-2576del
PGAP2 transcript variant X5	XM_047426777.1:c.337-2578=	XM_047426777.1:c.337-2577_337-2576del
PGAP2 transcript variant X6	XM_047426778.1:c.201-2530=	XM_047426778.1:c.201-2529_201-2528del
PGAP2 transcript variant X7	XM_047426779.1:c.-49-2578=	XM_047426779.1:c.-49-2577_-49-2576del
PGAP2 transcript variant X11	XM_047426780.1:c.162-2578=	XM_047426780.1:c.162-2577_162-2576del
PGAP2 transcript variant X15	XM_047426781.1:c.166-2578=	XM_047426781.1:c.166-2577_166-2576del
PGAP2 transcript variant X17	XM_047426782.1:c.161+6460=	XM_047426782.1:c.161+6461_161+6462del
PGAP2 transcript variant X20	XM_047426784.1:c.200+3351=	XM_047426784.1:c.200+3352_200+3353del
PGAP2 transcript variant X21	XM_047426785.1:c.200+3351=	XM_047426785.1:c.200+3352_200+3353del
PGAP2 transcript variant X22	XM_047426786.1:c.-15-2578=	XM_047426786.1:c.-15-2577_-15-2576del
PGAP2 transcript variant X23	XM_047426787.1:c.-15-2578=	XM_047426787.1:c.-15-2577_-15-2576del
PGAP2 transcript variant X24	XM_047426788.1:c.143+6460=	XM_047426788.1:c.143+6461_143+6462del
PGAP2 transcript variant X25	XM_047426789.1:c.-39+6460=	XM_047426789.1:c.-39+6461_-39+6462del
PGAP2 transcript variant X26	XM_047426790.1:c.-39+6124=	XM_047426790.1:c.-39+6125_-39+6126del
PGAP2 transcript variant X27	XM_047426792.1:c.-39+6460=	XM_047426792.1:c.-39+6461_-39+6462del
PGAP2 transcript variant X28	XM_047426793.1:c.143+6460=	XM_047426793.1:c.143+6461_143+6462del

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#.

2 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SWEGEN	ss3007499498	Jan 10, 2018 (151)
2	GNOMAD	ss4229114489	Apr 27, 2021 (155)
3	gnomAD - Genomes	NC_000011.10 - 3814775	Apr 27, 2021 (155)
4	ALFA	NC_000011.10 - 3814775	Apr 27, 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
ss3007499498	NC_000011.9:3836004:TC:	NC_000011.10:3814774:TCT:T	(self)
369782307, ss4229114489	NC_000011.10:3814774:TC:	NC_000011.10:3814774:TCT:T	(self)
197420588	NC_000011.10:3814774:TCT:T	NC_000011.10:3814774:TCT:T	(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 rs1491380005

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
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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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1491380005