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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.

rs2500430

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:25298327 (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 / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.474725 (125655/264690, TOPMED)
G=0.475845 (66448/139642, GnomAD)
A=0.00446 (126/28252, 14KJPN) (+ 15 more)
G=0.48094 (9082/18884, ALFA)
A=0.00412 (69/16756, 8.3KJPN)
A=0.4474 (2865/6404, 1000G_30x)
A=0.4313 (2160/5008, 1000G)
A=0.4696 (2102/4476, Estonian)
G=0.4720 (1819/3854, ALSPAC)
G=0.4846 (1797/3708, TWINSUK)
A=0.0034 (10/2928, KOREAN)
A=0.0027 (5/1832, Korea1K)
G=0.496 (495/998, GoNL)
G=0.435 (261/600, NorthernSweden)
A=0.265 (114/430, SGDP_PRJ)
G=0.454 (98/216, Qatari)
A=0.35 (17/48, Siberian)
G=0.45 (18/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABHD12 : Intron Variant
PYGB : 500B Downstream 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 18884 A=0.51906 G=0.48094
European Sub 14280 A=0.51057 G=0.48943
African Sub 2946 A=0.5536 G=0.4464
African Others Sub 114 A=0.570 G=0.430
African American Sub 2832 A=0.5530 G=0.4470
Asian Sub 112 A=0.009 G=0.991
East Asian Sub 86 A=0.01 G=0.99
Other Asian Sub 26 A=0.00 G=1.00
Latin American 1 Sub 146 A=0.596 G=0.404
Latin American 2 Sub 610 A=0.626 G=0.374
South Asian Sub 98 A=0.49 G=0.51
Other Sub 692 A=0.523 G=0.477


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=0.525275 G=0.474725
gnomAD - Genomes Global Study-wide 139642 A=0.524155 G=0.475845
gnomAD - Genomes European Sub 75612 A=0.51201 G=0.48799
gnomAD - Genomes African Sub 41826 A=0.55733 G=0.44267
gnomAD - Genomes American Sub 13624 A=0.57876 G=0.42124
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.6396 G=0.3604
gnomAD - Genomes East Asian Sub 3124 A=0.0115 G=0.9885
gnomAD - Genomes Other Sub 2140 A=0.5266 G=0.4734
14KJPN JAPANESE Study-wide 28252 A=0.00446 G=0.99554
Allele Frequency Aggregator Total Global 18884 A=0.51906 G=0.48094
Allele Frequency Aggregator European Sub 14280 A=0.51057 G=0.48943
Allele Frequency Aggregator African Sub 2946 A=0.5536 G=0.4464
Allele Frequency Aggregator Other Sub 692 A=0.523 G=0.477
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.626 G=0.374
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.596 G=0.404
Allele Frequency Aggregator Asian Sub 112 A=0.009 G=0.991
Allele Frequency Aggregator South Asian Sub 98 A=0.49 G=0.51
8.3KJPN JAPANESE Study-wide 16756 A=0.00412 G=0.99588
1000Genomes_30x Global Study-wide 6404 A=0.4474 G=0.5526
1000Genomes_30x African Sub 1786 A=0.5622 G=0.4378
1000Genomes_30x Europe Sub 1266 A=0.5197 G=0.4803
1000Genomes_30x South Asian Sub 1202 A=0.4792 G=0.5208
1000Genomes_30x East Asian Sub 1170 A=0.0222 G=0.9778
1000Genomes_30x American Sub 980 A=0.613 G=0.387
1000Genomes Global Study-wide 5008 A=0.4313 G=0.5687
1000Genomes African Sub 1322 A=0.5499 G=0.4501
1000Genomes East Asian Sub 1008 A=0.0228 G=0.9772
1000Genomes Europe Sub 1006 A=0.5189 G=0.4811
1000Genomes South Asian Sub 978 A=0.467 G=0.533
1000Genomes American Sub 694 A=0.621 G=0.379
Genetic variation in the Estonian population Estonian Study-wide 4476 A=0.4696 G=0.5304
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.5280 G=0.4720
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.5154 G=0.4846
KOREAN population from KRGDB KOREAN Study-wide 2928 A=0.0034 G=0.9966, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.0027 G=0.9973
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.504 G=0.496
Northern Sweden ACPOP Study-wide 600 A=0.565 G=0.435
SGDP_PRJ Global Study-wide 430 A=0.265 G=0.735
Qatari Global Study-wide 216 A=0.546 G=0.454
Siberian Global Study-wide 48 A=0.35 G=0.65
The Danish reference pan genome Danish Study-wide 40 A=0.55 G=0.45
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 20 NC_000020.11:g.25298327A>G
GRCh38.p14 chr 20 NC_000020.11:g.25298327A>T
GRCh37.p13 chr 20 NC_000020.10:g.25278963A>G
GRCh37.p13 chr 20 NC_000020.10:g.25278963A>T
ABHD12 RefSeqGene NG_028119.1:g.97656T>C
ABHD12 RefSeqGene NG_028119.1:g.97656T>A
Gene: ABHD12, abhydrolase domain containing 12, lysophospholipase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ABHD12 transcript variant 2 NM_015600.5:c.1158-3297T>C N/A Intron Variant
ABHD12 transcript variant 1 NM_001042472.3:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X2 XM_011529214.3:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X9 XM_017027797.3:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X1 XM_047440087.1:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X3 XM_047440088.1:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X4 XM_047440089.1:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X5 XM_047440090.1:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X6 XM_047440091.1:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X7 XM_047440092.1:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X8 XM_047440093.1:c. N/A Genic Downstream Transcript Variant
ABHD12 transcript variant X10 XM_047440094.1:c. N/A Genic Downstream Transcript Variant
Gene: PYGB, glycogen phosphorylase B (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
PYGB transcript NM_002862.4:c. N/A Downstream Transcript Variant
PYGB transcript variant X1 XM_047440342.1:c. N/A N/A
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.

Not Reported in ClinVar
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 T
GRCh38.p14 chr 20 NC_000020.11:g.25298327= NC_000020.11:g.25298327A>G NC_000020.11:g.25298327A>T
GRCh37.p13 chr 20 NC_000020.10:g.25278963= NC_000020.10:g.25278963A>G NC_000020.10:g.25278963A>T
ABHD12 RefSeqGene NG_028119.1:g.97656= NG_028119.1:g.97656T>C NG_028119.1:g.97656T>A
ABHD12 transcript variant 2 NM_015600.4:c.1158-3297= NM_015600.4:c.1158-3297T>C NM_015600.4:c.1158-3297T>A
ABHD12 transcript variant 2 NM_015600.5:c.1158-3297= NM_015600.5:c.1158-3297T>C NM_015600.5:c.1158-3297T>A
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#.

65 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3507177 Sep 28, 2001 (100)
2 SC_SNP ss8442679 Apr 21, 2003 (114)
3 CSHL-HAPMAP ss16887118 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss20121463 Feb 27, 2004 (120)
5 ABI ss41405166 Mar 14, 2006 (126)
6 HGSV ss83243397 Dec 14, 2007 (130)
7 IGMI-SNU ss115467416 Feb 04, 2009 (130)
8 ENSEMBL ss133026741 Dec 01, 2009 (131)
9 GMI ss156299634 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss169418996 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss172027546 Jul 04, 2010 (132)
12 BUSHMAN ss203865675 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss208739165 Jul 04, 2010 (132)
14 GMI ss283343351 May 04, 2012 (137)
15 PJP ss292636664 May 09, 2011 (134)
16 1000GENOMES ss340691310 May 09, 2011 (134)
17 TISHKOFF ss566210054 Apr 25, 2013 (138)
18 SSMP ss662083001 Apr 25, 2013 (138)
19 EVA-GONL ss994658165 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1082161453 Aug 21, 2014 (142)
21 1000GENOMES ss1364506893 Aug 21, 2014 (142)
22 DDI ss1429030456 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1579484541 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1638650910 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1681644943 Apr 01, 2015 (144)
26 HAMMER_LAB ss1809474675 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1938165882 Feb 12, 2016 (147)
28 JJLAB ss2029868323 Sep 14, 2016 (149)
29 USC_VALOUEV ss2158420375 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2242224409 Dec 20, 2016 (150)
31 SYSTEMSBIOZJU ss2629428801 Nov 08, 2017 (151)
32 GRF ss2704097560 Nov 08, 2017 (151)
33 GNOMAD ss2966658593 Nov 08, 2017 (151)
34 SWEGEN ss3018041559 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3028766713 Nov 08, 2017 (151)
36 CSHL ss3352471309 Nov 08, 2017 (151)
37 URBANLAB ss3650995451 Oct 12, 2018 (152)
38 EGCUT_WGS ss3684768267 Jul 13, 2019 (153)
39 EVA_DECODE ss3706776152 Jul 13, 2019 (153)
40 ACPOP ss3743343837 Jul 13, 2019 (153)
41 EVA ss3758563829 Jul 13, 2019 (153)
42 PACBIO ss3788628802 Jul 13, 2019 (153)
43 PACBIO ss3793524808 Jul 13, 2019 (153)
44 PACBIO ss3798411995 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3821729969 Jul 13, 2019 (153)
46 EVA ss3835644366 Apr 27, 2020 (154)
47 EVA ss3841448524 Apr 27, 2020 (154)
48 EVA ss3846956777 Apr 27, 2020 (154)
49 SGDP_PRJ ss3888961893 Apr 27, 2020 (154)
50 KRGDB ss3939169829 Apr 27, 2020 (154)
51 KOGIC ss3982025192 Apr 27, 2020 (154)
52 TOPMED ss5086099971 Apr 27, 2021 (155)
53 TOMMO_GENOMICS ss5229324489 Apr 27, 2021 (155)
54 1000G_HIGH_COVERAGE ss5308464362 Oct 16, 2022 (156)
55 HUGCELL_USP ss5500829691 Oct 16, 2022 (156)
56 EVA ss5512196248 Oct 16, 2022 (156)
57 1000G_HIGH_COVERAGE ss5614743294 Oct 16, 2022 (156)
58 SANFORD_IMAGENETICS ss5663084474 Oct 16, 2022 (156)
59 TOMMO_GENOMICS ss5788448596 Oct 16, 2022 (156)
60 YY_MCH ss5817910961 Oct 16, 2022 (156)
61 EVA ss5845596114 Oct 16, 2022 (156)
62 EVA ss5853116093 Oct 16, 2022 (156)
63 EVA ss5923120471 Oct 16, 2022 (156)
64 EVA ss5958002094 Oct 16, 2022 (156)
65 EVA ss5981082629 Oct 16, 2022 (156)
66 1000Genomes NC_000020.10 - 25278963 Oct 12, 2018 (152)
67 1000Genomes_30x NC_000020.11 - 25298327 Oct 16, 2022 (156)
68 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 25278963 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000020.10 - 25278963 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000020.10 - 25278963 Apr 27, 2020 (154)
71 gnomAD - Genomes NC_000020.11 - 25298327 Apr 27, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000020.10 - 25278963 Apr 27, 2020 (154)
73 KOREAN population from KRGDB NC_000020.10 - 25278963 Apr 27, 2020 (154)
74 Korean Genome Project NC_000020.11 - 25298327 Apr 27, 2020 (154)
75 Northern Sweden NC_000020.10 - 25278963 Jul 13, 2019 (153)
76 Qatari NC_000020.10 - 25278963 Apr 27, 2020 (154)
77 SGDP_PRJ NC_000020.10 - 25278963 Apr 27, 2020 (154)
78 Siberian NC_000020.10 - 25278963 Apr 27, 2020 (154)
79 8.3KJPN NC_000020.10 - 25278963 Apr 27, 2021 (155)
80 14KJPN NC_000020.11 - 25298327 Oct 16, 2022 (156)
81 TopMed NC_000020.11 - 25298327 Apr 27, 2021 (155)
82 UK 10K study - Twins NC_000020.10 - 25278963 Oct 12, 2018 (152)
83 ALFA NC_000020.11 - 25298327 Apr 27, 2021 (155)
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).

Associated ID History Updated (Build)
rs57543506 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83243397, ss169418996, ss172027546, ss203865675, ss208739165, ss283343351, ss292636664 NC_000020.9:25226962:A:G NC_000020.11:25298326:A:G (self)
77961013, 43165010, 30506515, 5649480, 19233956, 46347223, 16628702, 20207804, 40978873, 10936729, 87293796, 43165010, ss340691310, ss566210054, ss662083001, ss994658165, ss1082161453, ss1364506893, ss1429030456, ss1579484541, ss1638650910, ss1681644943, ss1809474675, ss1938165882, ss2029868323, ss2158420375, ss2629428801, ss2704097560, ss2966658593, ss3018041559, ss3352471309, ss3684768267, ss3743343837, ss3758563829, ss3788628802, ss3793524808, ss3798411995, ss3835644366, ss3841448524, ss3888961893, ss3939169829, ss5229324489, ss5512196248, ss5663084474, ss5845596114, ss5958002094, ss5981082629 NC_000020.10:25278962:A:G NC_000020.11:25298326:A:G (self)
102269229, 549601781, 38403193, 122285700, 361208916, 15165562717, ss2242224409, ss3028766713, ss3650995451, ss3706776152, ss3821729969, ss3846956777, ss3982025192, ss5086099971, ss5308464362, ss5500829691, ss5614743294, ss5788448596, ss5817910961, ss5853116093, ss5923120471 NC_000020.11:25298326:A:G NC_000020.11:25298326:A:G (self)
ss3507177, ss8442679, ss16887118, ss20121463, ss41405166, ss115467416, ss133026741, ss156299634 NT_011387.8:25218962:A:G NC_000020.11:25298326:A:G (self)
46347223, ss3939169829 NC_000020.10:25278962:A:T NC_000020.11:25298326:A:T (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 rs2500430
PMID Title Author Year Journal
31666285 Common and Rare Sequence Variants Influencing Tumor Biomarkers in Blood. Olafsson S et al. 2020 Cancer epidemiology, biomarkers & prevention
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