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dbSNP Short Genetic Variations

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.

rs1798082

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:71171531 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.101696 (26918/264690, TOPMED)
C=0.095569 (13390/140108, GnomAD)
C=0.06818 (2104/30860, ALFA) (+ 13 more)
C=0.00004 (1/28258, 14KJPN)
C=0.00006 (1/16760, 8.3KJPN)
C=0.1026 (657/6404, 1000G_30x)
C=0.0968 (485/5008, 1000G)
C=0.0199 (89/4480, Estonian)
C=0.0535 (206/3854, ALSPAC)
C=0.0556 (206/3708, TWINSUK)
C=0.0005 (1/1832, Korea1K)
C=0.042 (42/998, GoNL)
C=0.042 (25/600, NorthernSweden)
C=0.120 (39/326, HapMap)
C=0.093 (20/216, Qatari)
T=0.47 (32/68, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 30860 T=0.93182 C=0.06818
European Sub 24734 T=0.95027 C=0.04973
African Sub 3168 T=0.7942 C=0.2058
African Others Sub 124 T=0.710 C=0.290
African American Sub 3044 T=0.7976 C=0.2024
Asian Sub 128 T=1.000 C=0.000
East Asian Sub 100 T=1.00 C=0.00
Other Asian Sub 28 T=1.00 C=0.00
Latin American 1 Sub 168 T=0.893 C=0.107
Latin American 2 Sub 700 T=0.947 C=0.053
South Asian Sub 114 T=0.947 C=0.053
Other Sub 1848 T=0.9129 C=0.0871


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 T=0.898304 C=0.101696
gnomAD - Genomes Global Study-wide 140108 T=0.904431 C=0.095569
gnomAD - Genomes European Sub 75930 T=0.95471 C=0.04529
gnomAD - Genomes African Sub 41942 T=0.79805 C=0.20195
gnomAD - Genomes American Sub 13634 T=0.92863 C=0.07137
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.9021 C=0.0979
gnomAD - Genomes East Asian Sub 3130 T=0.9997 C=0.0003
gnomAD - Genomes Other Sub 2152 T=0.9154 C=0.0846
Allele Frequency Aggregator Total Global 30860 T=0.93182 C=0.06818
Allele Frequency Aggregator European Sub 24734 T=0.95027 C=0.04973
Allele Frequency Aggregator African Sub 3168 T=0.7942 C=0.2058
Allele Frequency Aggregator Other Sub 1848 T=0.9129 C=0.0871
Allele Frequency Aggregator Latin American 2 Sub 700 T=0.947 C=0.053
Allele Frequency Aggregator Latin American 1 Sub 168 T=0.893 C=0.107
Allele Frequency Aggregator Asian Sub 128 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 114 T=0.947 C=0.053
14KJPN JAPANESE Study-wide 28258 T=0.99996 C=0.00004
8.3KJPN JAPANESE Study-wide 16760 T=0.99994 C=0.00006
1000Genomes_30x Global Study-wide 6404 T=0.8974 C=0.1026
1000Genomes_30x African Sub 1786 T=0.7447 C=0.2553
1000Genomes_30x Europe Sub 1266 T=0.9447 C=0.0553
1000Genomes_30x South Asian Sub 1202 T=0.9493 C=0.0507
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.929 C=0.071
1000Genomes Global Study-wide 5008 T=0.9032 C=0.0968
1000Genomes African Sub 1322 T=0.7474 C=0.2526
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9493 C=0.0507
1000Genomes South Asian Sub 978 T=0.948 C=0.052
1000Genomes American Sub 694 T=0.929 C=0.071
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9801 C=0.0199
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9465 C=0.0535
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9444 C=0.0556
Korean Genome Project KOREAN Study-wide 1832 T=0.9995 C=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.958 C=0.042
Northern Sweden ACPOP Study-wide 600 T=0.958 C=0.042
HapMap Global Study-wide 326 T=0.880 C=0.120
HapMap African Sub 120 T=0.758 C=0.242
HapMap American Sub 120 T=0.917 C=0.083
HapMap Asian Sub 86 T=1.00 C=0.00
Qatari Global Study-wide 216 T=0.907 C=0.093
SGDP_PRJ Global Study-wide 68 T=0.47 C=0.53
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 12 NC_000012.12:g.71171531T>C
GRCh37.p13 chr 12 NC_000012.11:g.71565311T>C
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 T= C
GRCh38.p14 chr 12 NC_000012.12:g.71171531= NC_000012.12:g.71171531T>C
GRCh37.p13 chr 12 NC_000012.11:g.71565311= NC_000012.11:g.71565311T>C
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#.

55 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss2665664 Nov 09, 2000 (89)
2 ABI ss40164901 Mar 15, 2006 (126)
3 1000GENOMES ss113724812 Jan 25, 2009 (130)
4 ILLUMINA-UK ss118897384 Feb 14, 2009 (130)
5 COMPLETE_GENOMICS ss170204260 Jul 04, 2010 (132)
6 BUSHMAN ss198371104 Jul 04, 2010 (132)
7 1000GENOMES ss225820956 Jul 14, 2010 (132)
8 1000GENOMES ss235984330 Jul 15, 2010 (132)
9 PJP ss291278470 May 09, 2011 (134)
10 ILLUMINA ss479537767 May 04, 2012 (137)
11 ILLUMINA ss483103052 May 04, 2012 (137)
12 ILLUMINA ss533071634 Sep 08, 2015 (146)
13 TISHKOFF ss563244215 Apr 25, 2013 (138)
14 SSMP ss658809941 Apr 25, 2013 (138)
15 ILLUMINA ss779605315 Sep 08, 2015 (146)
16 ILLUMINA ss781006323 Sep 08, 2015 (146)
17 ILLUMINA ss835077403 Sep 08, 2015 (146)
18 EVA-GONL ss989672745 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1078561154 Aug 21, 2014 (142)
20 1000GENOMES ss1345552591 Aug 21, 2014 (142)
21 DDI ss1426974610 Apr 01, 2015 (144)
22 EVA_DECODE ss1599351658 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1628869419 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1671863452 Apr 01, 2015 (144)
25 HAMMER_LAB ss1807303761 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1933036315 Feb 12, 2016 (147)
27 JJLAB ss2027269036 Sep 14, 2016 (149)
28 HUMAN_LONGEVITY ss2190891067 Dec 20, 2016 (150)
29 ILLUMINA ss2632976160 Nov 08, 2017 (151)
30 GRF ss2699962143 Nov 08, 2017 (151)
31 GNOMAD ss2912061932 Nov 08, 2017 (151)
32 SWEGEN ss3009910752 Nov 08, 2017 (151)
33 CSHL ss3350126044 Nov 08, 2017 (151)
34 ILLUMINA ss3626909223 Oct 12, 2018 (152)
35 ILLUMINA ss3630984397 Oct 12, 2018 (152)
36 ILLUMINA ss3641796922 Oct 12, 2018 (152)
37 EGCUT_WGS ss3677182079 Jul 13, 2019 (153)
38 EVA_DECODE ss3693933783 Jul 13, 2019 (153)
39 ACPOP ss3739139129 Jul 13, 2019 (153)
40 KHV_HUMAN_GENOMES ss3815973797 Jul 13, 2019 (153)
41 EVA ss3833190731 Apr 27, 2020 (154)
42 SGDP_PRJ ss3878554287 Apr 27, 2020 (154)
43 KOGIC ss3972203242 Apr 27, 2020 (154)
44 TOPMED ss4923064813 Apr 26, 2021 (155)
45 TOMMO_GENOMICS ss5206938071 Apr 26, 2021 (155)
46 1000G_HIGH_COVERAGE ss5291283601 Oct 16, 2022 (156)
47 EVA ss5406493270 Oct 16, 2022 (156)
48 HUGCELL_USP ss5485980415 Oct 16, 2022 (156)
49 EVA ss5510750807 Oct 16, 2022 (156)
50 1000G_HIGH_COVERAGE ss5589009705 Oct 16, 2022 (156)
51 SANFORD_IMAGENETICS ss5653419875 Oct 16, 2022 (156)
52 TOMMO_GENOMICS ss5756910729 Oct 16, 2022 (156)
53 EVA ss5838147301 Oct 16, 2022 (156)
54 EVA ss5904927280 Oct 16, 2022 (156)
55 EVA ss5944792871 Oct 16, 2022 (156)
56 1000Genomes NC_000012.11 - 71565311 Oct 12, 2018 (152)
57 1000Genomes_30x NC_000012.12 - 71171531 Oct 16, 2022 (156)
58 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 71565311 Oct 12, 2018 (152)
59 Genetic variation in the Estonian population NC_000012.11 - 71565311 Oct 12, 2018 (152)
60 gnomAD - Genomes NC_000012.12 - 71171531 Apr 26, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000012.11 - 71565311 Apr 27, 2020 (154)
62 HapMap NC_000012.12 - 71171531 Apr 27, 2020 (154)
63 Korean Genome Project NC_000012.12 - 71171531 Apr 27, 2020 (154)
64 Northern Sweden NC_000012.11 - 71565311 Jul 13, 2019 (153)
65 Qatari NC_000012.11 - 71565311 Apr 27, 2020 (154)
66 SGDP_PRJ NC_000012.11 - 71565311 Apr 27, 2020 (154)
67 8.3KJPN NC_000012.11 - 71565311 Apr 26, 2021 (155)
68 14KJPN NC_000012.12 - 71171531 Oct 16, 2022 (156)
69 TopMed NC_000012.12 - 71171531 Apr 26, 2021 (155)
70 UK 10K study - Twins NC_000012.11 - 71565311 Oct 12, 2018 (152)
71 ALFA NC_000012.12 - 71171531 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss113724812, ss118897384, ss170204260, ss198371104, ss291278470, ss483103052, ss1599351658 NC_000012.10:69851577:T:C NC_000012.12:71171530:T:C (self)
58321705, 32382324, 22920327, 14448250, 12423994, 15078245, 30571267, 64907378, 32382324, ss225820956, ss235984330, ss479537767, ss533071634, ss563244215, ss658809941, ss779605315, ss781006323, ss835077403, ss989672745, ss1078561154, ss1345552591, ss1426974610, ss1628869419, ss1671863452, ss1807303761, ss1933036315, ss2027269036, ss2632976160, ss2699962143, ss2912061932, ss3009910752, ss3350126044, ss3626909223, ss3630984397, ss3641796922, ss3677182079, ss3739139129, ss3833190731, ss3878554287, ss5206938071, ss5406493270, ss5510750807, ss5653419875, ss5838147301, ss5944792871 NC_000012.11:71565310:T:C NC_000012.12:71171530:T:C (self)
76535640, 411300898, 845870, 28581243, 90747833, 138610470, 10211009074, ss2190891067, ss3693933783, ss3815973797, ss3972203242, ss4923064813, ss5291283601, ss5485980415, ss5589009705, ss5756910729, ss5904927280 NC_000012.12:71171530:T:C NC_000012.12:71171530:T:C (self)
ss2665664, ss40164901 NT_029419.12:33708616:T:C NC_000012.12:71171530:T:C (self)
Help

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

No publications for rs1798082

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