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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs142192097

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:26794383 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.001035 (274/264690, TOPMED)
G=0.001388 (349/251466, GnomAD_exome)
G=0.001904 (388/203744, ALFA) (+ 7 more)
G=0.000970 (136/140218, GnomAD)
G=0.001582 (192/121400, ExAC)
G=0.00053 (42/78694, PAGE_STUDY)
G=0.0009 (6/6404, 1000G_30x)
G=0.0008 (4/5008, 1000G)
G=0.0002 (1/4480, Estonian)
G=0.002 (1/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PIGV : Missense Variant
Publications
1 citation
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 220250 A=0.998116 G=0.001884
European Sub 184610 A=0.997882 G=0.002118
African Sub 9792 A=0.9998 G=0.0002
African Others Sub 360 A=1.000 G=0.000
African American Sub 9432 A=0.9998 G=0.0002
Asian Sub 6350 A=1.0000 G=0.0000
East Asian Sub 4502 A=1.0000 G=0.0000
Other Asian Sub 1848 A=1.0000 G=0.0000
Latin American 1 Sub 796 A=1.000 G=0.000
Latin American 2 Sub 968 A=0.999 G=0.001
South Asian Sub 280 A=1.000 G=0.000
Other Sub 17454 A=0.99880 G=0.00120


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 A=0.998965 G=0.001035
gnomAD - Exomes Global Study-wide 251466 A=0.998612 G=0.001388
gnomAD - Exomes European Sub 135396 A=0.998050 G=0.001950
gnomAD - Exomes Asian Sub 49010 A=0.99992 G=0.00008
gnomAD - Exomes American Sub 34588 A=0.99910 G=0.00090
gnomAD - Exomes African Sub 16256 A=0.99963 G=0.00037
gnomAD - Exomes Ashkenazi Jewish Sub 10080 A=0.99692 G=0.00308
gnomAD - Exomes Other Sub 6136 A=0.9979 G=0.0021
Allele Frequency Aggregator Total Global 203744 A=0.998096 G=0.001904
Allele Frequency Aggregator European Sub 174394 A=0.997913 G=0.002087
Allele Frequency Aggregator Other Sub 16002 A=0.99869 G=0.00131
Allele Frequency Aggregator Asian Sub 6350 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 4954 A=0.9996 G=0.0004
Allele Frequency Aggregator Latin American 2 Sub 968 A=0.999 G=0.001
Allele Frequency Aggregator Latin American 1 Sub 796 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 280 A=1.000 G=0.000
gnomAD - Genomes Global Study-wide 140218 A=0.999030 G=0.000970
gnomAD - Genomes European Sub 75934 A=0.99868 G=0.00132
gnomAD - Genomes African Sub 42022 A=0.99962 G=0.00038
gnomAD - Genomes American Sub 13652 A=0.99956 G=0.00044
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9961 G=0.0039
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 A=0.9995 G=0.0005
ExAC Global Study-wide 121400 A=0.998418 G=0.001582
ExAC Europe Sub 73344 A=0.99770 G=0.00230
ExAC Asian Sub 25166 A=0.99988 G=0.00012
ExAC American Sub 11576 A=0.99888 G=0.00112
ExAC African Sub 10406 A=0.99942 G=0.00058
ExAC Other Sub 908 A=0.999 G=0.001
The PAGE Study Global Study-wide 78694 A=0.99947 G=0.00053
The PAGE Study AfricanAmerican Sub 32512 A=0.99963 G=0.00037
The PAGE Study Mexican Sub 10810 A=0.99954 G=0.00046
The PAGE Study Asian Sub 8316 A=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7918 A=0.9981 G=0.0019
The PAGE Study NativeHawaiian Sub 4534 A=0.9993 G=0.0007
The PAGE Study Cuban Sub 4228 A=0.9991 G=0.0009
The PAGE Study Dominican Sub 3828 A=0.9997 G=0.0003
The PAGE Study CentralAmerican Sub 2450 A=1.0000 G=0.0000
The PAGE Study SouthAmerican Sub 1982 A=0.9995 G=0.0005
The PAGE Study NativeAmerican Sub 1260 A=0.9992 G=0.0008
The PAGE Study SouthAsian Sub 856 A=1.000 G=0.000
1000Genomes_30x Global Study-wide 6404 A=0.9991 G=0.0009
1000Genomes_30x African Sub 1786 A=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 A=0.9984 G=0.0016
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.996 G=0.004
1000Genomes Global Study-wide 5008 A=0.9992 G=0.0008
1000Genomes African Sub 1322 A=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9980 G=0.0020
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.997 G=0.003
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9998 G=0.0002
Northern Sweden ACPOP Study-wide 600 A=0.998 G=0.002
Help

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 1 NC_000001.11:g.26794383A>G
GRCh37.p13 chr 1 NC_000001.10:g.27120874A>G
PIGV RefSeqGene NG_028133.1:g.11421A>G
Gene: PIGV, phosphatidylinositol glycan anchor biosynthesis class V (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PIGV transcript variant 8 NM_001374484.1:c.172+177A…

NM_001374484.1:c.172+177A>G

 		N/A Intron Variant
PIGV transcript variant 9 NM_001374485.1:c.172+177A…

NM_001374485.1:c.172+177A>G

 		N/A Intron Variant
PIGV transcript variant 10 NM_001374486.1:c.79-3180A…

NM_001374486.1:c.79-3180A>G

 		N/A Intron Variant
PIGV transcript variant 7 NM_001374483.1:c.-33= N/A 5 Prime UTR Variant
PIGV transcript variant 3 NM_001374478.1:c.349A>G I [ATT] > V [GTT] Coding Sequence Variant
GPI mannosyltransferase 2 isoform a NP_001361407.1:p.Ile117Val I (Ile) > V (Val) Missense Variant
PIGV transcript variant 2 NM_017837.4:c.349A>G I [ATT] > V [GTT] Coding Sequence Variant
GPI mannosyltransferase 2 isoform a NP_060307.2:p.Ile117Val I (Ile) > V (Val) Missense Variant
PIGV transcript variant 6 NM_001374482.1:c.349A>G I [ATT] > V [GTT] Coding Sequence Variant
GPI mannosyltransferase 2 isoform a NP_001361411.1:p.Ile117Val I (Ile) > V (Val) Missense Variant
PIGV transcript variant 4 NM_001374480.1:c.349A>G I [ATT] > V [GTT] Coding Sequence Variant
GPI mannosyltransferase 2 isoform a NP_001361409.1:p.Ile117Val I (Ile) > V (Val) Missense Variant
PIGV transcript variant 5 NM_001374481.1:c.349A>G I [ATT] > V [GTT] Coding Sequence Variant
GPI mannosyltransferase 2 isoform a NP_001361410.1:p.Ile117Val I (Ile) > V (Val) Missense Variant
PIGV transcript variant 1 NM_001202554.2:c.349A>G I [ATT] > V [GTT] Coding Sequence Variant
GPI mannosyltransferase 2 isoform a NP_001189483.1:p.Ile117Val I (Ile) > V (Val) Missense Variant
PIGV transcript variant 11 NR_164651.1:n.847A>G N/A Non Coding Transcript Variant
PIGV transcript variant 12 NR_164652.1:n. N/A Intron Variant
Help

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.

Allele: G (allele ID: 282186 )
ClinVar Accession Disease Names Clinical Significance
RCV000286962.4 Hyperphosphatasia with intellectual disability syndrome 1 Uncertain-Significance
RCV000455981.3 not specified Uncertain-Significance
RCV000514626.7 not provided Conflicting-Interpretations-Of-Pathogenicity
Help

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= G
GRCh38.p14 chr 1 NC_000001.11:g.26794383= NC_000001.11:g.26794383A>G
GRCh37.p13 chr 1 NC_000001.10:g.27120874= NC_000001.10:g.27120874A>G
PIGV RefSeqGene NG_028133.1:g.11421= NG_028133.1:g.11421A>G
PIGV transcript variant 2 NM_017837.4:c.349= NM_017837.4:c.349A>G
PIGV transcript variant 2 NM_017837.3:c.349= NM_017837.3:c.349A>G
PIGV transcript variant 1 NM_001202554.2:c.349= NM_001202554.2:c.349A>G
PIGV transcript variant 1 NM_001202554.1:c.349= NM_001202554.1:c.349A>G
PIGV transcript variant 4 NM_001374480.1:c.349= NM_001374480.1:c.349A>G
PIGV transcript variant 11 NR_164651.1:n.847= NR_164651.1:n.847A>G
PIGV transcript variant 5 NM_001374481.1:c.349= NM_001374481.1:c.349A>G
PIGV transcript variant 6 NM_001374482.1:c.349= NM_001374482.1:c.349A>G
PIGV transcript variant 3 NM_001374478.1:c.349= NM_001374478.1:c.349A>G
PIGV transcript variant 7 NM_001374483.1:c.-33= NM_001374483.1:c.-33A>G
GPI mannosyltransferase 2 isoform a NP_060307.2:p.Ile117= NP_060307.2:p.Ile117Val
GPI mannosyltransferase 2 isoform a NP_001189483.1:p.Ile117= NP_001189483.1:p.Ile117Val
GPI mannosyltransferase 2 isoform a NP_001361409.1:p.Ile117= NP_001361409.1:p.Ile117Val
GPI mannosyltransferase 2 isoform a NP_001361410.1:p.Ile117= NP_001361410.1:p.Ile117Val
GPI mannosyltransferase 2 isoform a NP_001361411.1:p.Ile117= NP_001361411.1:p.Ile117Val
GPI mannosyltransferase 2 isoform a NP_001361407.1:p.Ile117= NP_001361407.1:p.Ile117Val
PIGV transcript variant 8 NM_001374484.1:c.172+177= NM_001374484.1:c.172+177A>G
PIGV transcript variant 9 NM_001374485.1:c.172+177= NM_001374485.1:c.172+177A>G
PIGV transcript variant 10 NM_001374486.1:c.79-3180= NM_001374486.1:c.79-3180A>G
PIGV transcript variant X5 XM_005245940.1:c.84+177= XM_005245940.1:c.84+177A>G
Help

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#.

44 SubSNP, 10 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491289893 May 04, 2012 (137)
2 CLINSEQ_SNP ss491589803 May 04, 2012 (137)
3 ILLUMINA ss780822519 Sep 08, 2015 (146)
4 ILLUMINA ss783505014 Sep 08, 2015 (146)
5 1000GENOMES ss1290129025 Aug 21, 2014 (142)
6 EVA_DECODE ss1584328884 Apr 01, 2015 (144)
7 EVA_EXAC ss1685411722 Apr 01, 2015 (144)
8 ILLUMINA ss1751913521 Sep 08, 2015 (146)
9 ILLUMINA ss1917725355 Feb 12, 2016 (147)
10 ILLUMINA ss1945989104 Feb 12, 2016 (147)
11 ILLUMINA ss1958255672 Feb 12, 2016 (147)
12 HUMAN_LONGEVITY ss2160915754 Dec 20, 2016 (150)
13 GNOMAD ss2731284856 Nov 08, 2017 (151)
14 GNOMAD ss2746268163 Nov 08, 2017 (151)
15 GNOMAD ss2752942908 Nov 08, 2017 (151)
16 AFFY ss2984852115 Nov 08, 2017 (151)
17 SWEGEN ss2986504967 Nov 08, 2017 (151)
18 ILLUMINA ss3021069335 Nov 08, 2017 (151)
19 ILLUMINA ss3626054162 Oct 11, 2018 (152)
20 ILLUMINA ss3634314134 Oct 11, 2018 (152)
21 ILLUMINA ss3640021496 Oct 11, 2018 (152)
22 ILLUMINA ss3644484976 Oct 11, 2018 (152)
23 ILLUMINA ss3651394787 Oct 11, 2018 (152)
24 ILLUMINA ss3653624547 Oct 11, 2018 (152)
25 EGCUT_WGS ss3654569775 Jul 12, 2019 (153)
26 ILLUMINA ss3725008318 Jul 12, 2019 (153)
27 ACPOP ss3726888152 Jul 12, 2019 (153)
28 ILLUMINA ss3744342126 Jul 12, 2019 (153)
29 ILLUMINA ss3744615084 Jul 12, 2019 (153)
30 PAGE_CC ss3770795262 Jul 12, 2019 (153)
31 ILLUMINA ss3772116630 Jul 12, 2019 (153)
32 EVA ss3986109230 Apr 27, 2021 (155)
33 TOPMED ss4442957754 Apr 27, 2021 (155)
34 EVA ss5237631538 Oct 13, 2022 (156)
35 1000G_HIGH_COVERAGE ss5241593921 Oct 13, 2022 (156)
36 EVA ss5317489337 Oct 13, 2022 (156)
37 HUGCELL_USP ss5442734426 Oct 13, 2022 (156)
38 1000G_HIGH_COVERAGE ss5513542411 Oct 13, 2022 (156)
39 SANFORD_IMAGENETICS ss5625158367 Oct 13, 2022 (156)
40 EVA ss5831702001 Oct 13, 2022 (156)
41 EVA ss5847531052 Oct 13, 2022 (156)
42 EVA ss5848254170 Oct 13, 2022 (156)
43 EVA ss5907490823 Oct 13, 2022 (156)
44 EVA ss5936974837 Oct 13, 2022 (156)
45 1000Genomes NC_000001.10 - 27120874 Oct 11, 2018 (152)
46 1000Genomes_30x NC_000001.11 - 26794383 Oct 13, 2022 (156)
47 Genetic variation in the Estonian population NC_000001.10 - 27120874 Oct 11, 2018 (152)
48 ExAC NC_000001.10 - 27120874 Oct 11, 2018 (152)
49 gnomAD - Genomes NC_000001.11 - 26794383 Apr 27, 2021 (155)
50 gnomAD - Exomes NC_000001.10 - 27120874 Jul 12, 2019 (153)
51 Northern Sweden NC_000001.10 - 27120874 Jul 12, 2019 (153)
52 The PAGE Study NC_000001.11 - 26794383 Jul 12, 2019 (153)
53 TopMed NC_000001.11 - 26794383 Apr 27, 2021 (155)
54 ALFA NC_000001.11 - 26794383 Apr 27, 2021 (155)
55 ClinVar RCV000286962.4 Oct 13, 2022 (156)
56 ClinVar RCV000455981.3 Oct 13, 2022 (156)
57 ClinVar RCV000514626.7 Oct 13, 2022 (156)
Help

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
ss491589803, ss1584328884 NC_000001.9:26993460:A:G NC_000001.11:26794382:A:G (self)
820385, 308023, 4598461, 299241, 173017, ss491289893, ss780822519, ss783505014, ss1290129025, ss1685411722, ss1751913521, ss1917725355, ss1945989104, ss1958255672, ss2731284856, ss2746268163, ss2752942908, ss2984852115, ss2986504967, ss3021069335, ss3626054162, ss3634314134, ss3640021496, ss3644484976, ss3651394787, ss3653624547, ss3654569775, ss3726888152, ss3744342126, ss3744615084, ss3772116630, ss3986109230, ss5317489337, ss5625158367, ss5831702001, ss5847531052, ss5848254170, ss5936974837 NC_000001.10:27120873:A:G NC_000001.11:26794382:A:G (self)
RCV000286962.4, RCV000455981.3, RCV000514626.7, 1068346, 5751944, 16731, 6564089, 13294923848, ss2160915754, ss3725008318, ss3770795262, ss4442957754, ss5237631538, ss5241593921, ss5442734426, ss5513542411, ss5907490823 NC_000001.11:26794382:A:G NC_000001.11:26794382:A:G (self)
Help

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

1 citation for rs142192097
PMID Title Author Year Journal
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics
Help

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.

Software version is: 2.0.1.post761+d5e8e07