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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs1800932

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr2:47790942 (GRCh38.p7) 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=0.13481 (33198/246250, GnomAD)
G=0.14532 (18248/125568, TOPMED)
G=0.13495 (16382/121394, ExAC) (+ 5 more)
G=0.1314 (4068/30960, GnomAD)
G=0.1652 (2149/13006, GO-ESP)
G=0.087 (434/5008, 1000G)
G=0.196 (756/3854, ALSPAC)
G=0.189 (699/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MSH6 : Synonymous Variant
Publications
12 citations
Genomic View
See rs on genome
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.p7 chr 2 NC_000002.12:g.47790942A>G
GRCh37.p13 chr 2 NC_000002.11:g.48018081A>G
MSH6 RefSeqGene (LRG_219) NG_007111.1:g.12796A>G
Gene: MSH6, mutS homolog 6 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MSH6 transcript variant 2 NM_001281492.1:c. N/A Intron Variant
MSH6 transcript variant 3 NM_001281493.1:c. N/A 5 Prime UTR Variant
MSH6 transcript variant 4 NM_001281494.1:c. N/A 5 Prime UTR Variant
MSH6 transcript variant 1 NM_000179.2:c.276A>G P [CCA] > P [CCG] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 1 NP_000170.1:p.Pro92= P (Pro) > P (Pro) Synonymous Variant
MSH6 transcript variant X2 XM_011532799.1:c. N/A 5 Prime UTR Variant
MSH6 transcript variant X1 XM_011532798.1:c....

XM_011532798.1:c.93A>G

P [CCA] > P [CCG] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X1 XP_011531100.1:p....

XP_011531100.1:p.Pro31=

P (Pro) > P (Pro) Synonymous 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: 45249 )
ClinVar Accession Disease Names Clinical Significance
RCV000030265.4 Lynch syndrome Benign
RCV000035321.10 not specified Benign
RCV000162362.1 Hereditary cancer-predisposing syndrome Benign
RCV000616289.1 Hereditary nonpolyposis colorectal cancer type 5 Benign
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").

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Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 246250 A=0.86519 G=0.13481
The Genome Aggregation Database European Sub 134000 A=0.82086 G=0.17914
The Genome Aggregation Database Asian Sub 48030 A=0.9527 G=0.0473
The Genome Aggregation Database American Sub 33582 A=0.9145 G=0.0855
The Genome Aggregation Database African Sub 15302 A=0.8970 G=0.1030
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 A=0.828 G=0.172
The Genome Aggregation Database Other Sub 5486 A=0.858 G=0.142
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.85468 G=0.14532
The Exome Aggregation Consortium Global Study-wide 121394 A=0.86505 G=0.13495
The Exome Aggregation Consortium Europe Sub 73348 A=0.8229 G=0.1771
The Exome Aggregation Consortium Asian Sub 25166 A=0.9510 G=0.0490
The Exome Aggregation Consortium American Sub 11570 A=0.9197 G=0.0803
The Exome Aggregation Consortium African Sub 10402 A=0.8942 G=0.1058
The Exome Aggregation Consortium Other Sub 908 A=0.86 G=0.14
The Genome Aggregation Database Global Study-wide 30960 A=0.8686 G=0.1314
The Genome Aggregation Database European Sub 18486 A=0.8444 G=0.1556
The Genome Aggregation Database African Sub 8730 A=0.892 G=0.108
The Genome Aggregation Database East Asian Sub 1622 A=0.999 G=0.001
The Genome Aggregation Database Other Sub 982 A=0.88 G=0.12
The Genome Aggregation Database American Sub 838 A=0.90 G=0.10
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=0.85 G=0.15
GO Exome Sequencing Project Global Study-wide 13006 A=0.8348 G=0.1652
GO Exome Sequencing Project European American Sub 8600 A=0.810 G=0.190
GO Exome Sequencing Project African American Sub 4406 A=0.884 G=0.116
1000Genomes Global Study-wide 5008 A=0.913 G=0.087
1000Genomes African Sub 1322 A=0.916 G=0.084
1000Genomes East Asian Sub 1008 A=1.000 G=0.000
1000Genomes Europe Sub 1006 A=0.821 G=0.179
1000Genomes South Asian Sub 978 A=0.94 G=0.06
1000Genomes American Sub 694 A=0.88 G=0.12
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.804 G=0.196
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.811 G=0.189
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 Note
GRCh38.p7 chr 2 NC_000002.12:g.47790942A= NC_000002.12:g.47790942A>G
GRCh37.p13 chr 2 NC_000002.11:g.48018081A= NC_000002.11:g.48018081A>G
MSH6 RefSeqGene (LRG_219) NG_007111.1:g.12796A= NG_007111.1:g.12796A>G
MSH6 transcript variant 1 NM_000179.2:c.276A= NM_000179.2:c.276A>G
MSH6 transcript variant 3 NM_001281493.1:c.-461A= NM_001281493.1:c.-461A>G
MSH6 transcript variant 4 NM_001281494.1:c.-627A= NM_001281494.1:c.-627A>G
MSH6 transcript variant X2 XM_011532799.1:c.-22A= XM_011532799.1:c.-22A>G
MSH6 transcript variant X1 XM_011532798.1:c.93A= XM_011532798.1:c.93A>G
DNA mismatch repair protein Msh6 isoform 1 NP_000170.1:p.Pro92= NP_000170.1:p.Pro92=
DNA mismatch repair protein Msh6 isoform X1 XP_011531100.1:p.Pro31= XP_011531100.1:p.Pro31=
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#.

4 ClinVar, 8 Frequency, 70 SubSNP submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2421091 Nov 14, 2000 (89)
2 UWGC ss2924021 Sep 28, 2001 (101)
3 EGP_SNPS ss4384536 Mar 26, 2002 (103)
4 PERLEGEN ss24636615 Sep 20, 2004 (123)
5 MGC_GENOME_DIFF ss28497392 Sep 24, 2004 (126)
6 MGC_GENOME_DIFF ss28512071 Sep 24, 2004 (126)
7 ICRCG ss37042835 May 24, 2005 (125)
8 APPLERA_GI ss48411758 Mar 11, 2006 (126)
9 AFFY ss66049817 Nov 30, 2006 (127)
10 PERLEGEN ss68813168 May 17, 2007 (127)
11 AFFY ss75953557 Dec 06, 2007 (129)
12 CGM_KYOTO ss76862477 Dec 06, 2007 (129)
13 KRIBB_YJKIM ss81586979 Dec 14, 2007 (130)
14 HGSV ss85349805 Dec 15, 2007 (130)
15 CANCER-GENOME ss86344850 Mar 23, 2008 (129)
16 SEATTLESEQ ss159701918 Dec 01, 2009 (131)
17 ILLUMINA ss160462944 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss166557405 Jul 04, 2010 (132)
19 AFFY ss169611740 Jul 04, 2010 (132)
20 BUSHMAN ss200401922 Jul 04, 2010 (132)
21 1000GENOMES ss219227424 Jul 14, 2010 (132)
22 1000GENOMES ss231154272 Jul 14, 2010 (132)
23 BL ss253089202 May 09, 2011 (134)
24 PJP ss292262970 May 09, 2011 (134)
25 NHLBI-ESP ss342059112 May 09, 2011 (134)
26 CORRELAGEN ss472343121 Nov 18, 2011 (136)
27 ILLUMINA ss481067570 Sep 08, 2015 (146)
28 ILLUMINA ss483840778 May 04, 2012 (137)
29 ILLUMINA ss484093102 May 04, 2012 (137)
30 1000GENOMES ss489815230 May 04, 2012 (137)
31 CLINSEQ_SNP ss491783030 May 04, 2012 (137)
32 ILLUMINA ss536036912 Sep 08, 2015 (146)
33 MMR_WOODS ss538293019 Oct 24, 2012 (137)
34 TISHKOFF ss555541777 Apr 25, 2013 (138)
35 SSMP ss649124908 Apr 25, 2013 (138)
36 ILLUMINA ss779518221 Sep 08, 2015 (146)
37 ILLUMINA ss782363955 Sep 08, 2015 (146)
38 ILLUMINA ss834988669 Sep 08, 2015 (146)
39 JMKIDD_LAB ss974442149 Aug 21, 2014 (142)
40 EVA-GONL ss976788862 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1067437182 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1069084403 Aug 21, 2014 (142)
43 1000GENOMES ss1297064484 Aug 21, 2014 (142)
44 HAMMER_LAB ss1397291090 Sep 08, 2015 (146)
45 DDI ss1428566343 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1578862571 Apr 01, 2015 (144)
47 EVA_FINRISK ss1584018434 Apr 01, 2015 (144)
48 EVA_DECODE ss1586199171 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1603424523 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1646418556 Apr 01, 2015 (144)
51 EVA_EXAC ss1686300566 Apr 01, 2015 (144)
52 EVA_MGP ss1710962479 Apr 01, 2015 (144)
53 EVA_SVP ss1712453049 Apr 01, 2015 (144)
54 HAMMER_LAB ss1796709754 Sep 08, 2015 (146)
55 WEILL_CORNELL_DGM ss1920024216 Feb 12, 2016 (147)
56 JJLAB ss2020545477 Sep 14, 2016 (149)
57 USC_VALOUEV ss2148589782 Dec 20, 2016 (150)
58 HUMAN_LONGEVITY ss2229920160 Dec 20, 2016 (150)
59 TOPMED ss2395850133 Dec 20, 2016 (150)
60 ILLUMINA ss2633609762 Nov 08, 2017 (151)
61 GNOMAD ss2732653643 Nov 08, 2017 (151)
62 GNOMAD ss2746676853 Nov 08, 2017 (151)
63 GNOMAD ss2772977414 Nov 08, 2017 (151)
64 SWEGEN ss2989438055 Nov 08, 2017 (151)
65 BIOINF_KMB_FNS_UNIBA ss3024038476 Nov 08, 2017 (151)
66 TOPMED ss3306786969 Nov 08, 2017 (151)
67 CSHL ss3344210989 Nov 08, 2017 (151)
68 ILLUMINA ss3628056112 Jul 19, 2018 (151)
69 ILLUMINA ss3631577049 Jul 19, 2018 (151)
70 ILLUMINA ss3636450881 Jul 19, 2018 (151)
71 1000Genomes NC_000002.11 - 48018081 Jul 19, 2018 (151)
72 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 48018081 Jul 19, 2018 (151)
73 The Exome Aggregation Consortium NC_000002.11 - 48018081 Jul 19, 2018 (151)
74 The Genome Aggregation Database NC_000002.11 - 48018081 Jul 19, 2018 (151)
75 The Genome Aggregation Database NC_000002.11 - 48018081 Jul 19, 2018 (151)
76 GO Exome Sequencing Project NC_000002.11 - 48018081 Jul 19, 2018 (151)
77 Trans-Omics for Precision Medicine NC_000002.12 - 47790942 Jul 19, 2018 (151)
78 UK 10K study - Twins NC_000002.11 - 48018081 Jul 19, 2018 (151)
79 ClinVar RCV000030265.4 Jul 19, 2018 (151)
80 ClinVar RCV000035321.10 Jul 19, 2018 (151)
81 ClinVar RCV000162362.1 Jul 19, 2018 (151)
82 ClinVar RCV000616289.1 Jul 19, 2018 (151)
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)
rs2266739 Nov 05, 2001 (101)
rs17395460 Oct 07, 2004 (123)
rs17845007 Mar 11, 2006 (126)
rs17857769 Mar 11, 2006 (126)
rs56716124 Feb 27, 2009 (130)
rs59593633 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss85349805 NC_000002.9:47929731:A= NC_000002.12:47790941:A= (self)
ss66049817, ss75953557, ss166557405, ss169611740, ss200401922, ss253089202, ss292262970, ss484093102, ss491783030, ss1397291090, ss1586199171, ss1712453049 NC_000002.10:47871584:A= NC_000002.12:47790941:A= (self)
8003762, 4447656, 6170233, 102467275, 1668378, 226398, 4447656, ss219227424, ss231154272, ss342059112, ss481067570, ss483840778, ss489815230, ss536036912, ss555541777, ss649124908, ss779518221, ss782363955, ss834988669, ss974442149, ss976788862, ss1067437182, ss1069084403, ss1297064484, ss1428566343, ss1578862571, ss1584018434, ss1603424523, ss1646418556, ss1686300566, ss1710962479, ss1796709754, ss1920024216, ss2020545477, ss2148589782, ss2395850133, ss2633609762, ss2732653643, ss2746676853, ss2772977414, ss2989438055, ss3344210989, ss3628056112, ss3631577049, ss3636450881 NC_000002.11:48018080:A= NC_000002.12:47790941:A= (self)
192129474, ss472343121, ss538293019, ss2229920160, ss3024038476, ss3306786969 NC_000002.12:47790941:A= NC_000002.12:47790941:A= (self)
ss2421091, ss2924021, ss4384536, ss24636615, ss28497392, ss28512071, ss37042835, ss48411758, ss68813168, ss76862477, ss81586979, ss86344850, ss159701918, ss160462944 NT_022184.15:26839967:A= NC_000002.12:47790941:A= (self)
ss85349805 NC_000002.9:47929731:A>G NC_000002.12:47790941:A>G (self)
ss66049817, ss75953557, ss166557405, ss169611740, ss200401922, ss253089202, ss292262970, ss484093102, ss491783030, ss1397291090, ss1586199171, ss1712453049 NC_000002.10:47871584:A>G NC_000002.12:47790941:A>G (self)
8003762, 4447656, 6170233, 102467275, 1668378, 226398, 4447656, ss219227424, ss231154272, ss342059112, ss481067570, ss483840778, ss489815230, ss536036912, ss555541777, ss649124908, ss779518221, ss782363955, ss834988669, ss974442149, ss976788862, ss1067437182, ss1069084403, ss1297064484, ss1428566343, ss1578862571, ss1584018434, ss1603424523, ss1646418556, ss1686300566, ss1710962479, ss1796709754, ss1920024216, ss2020545477, ss2148589782, ss2395850133, ss2633609762, ss2732653643, ss2746676853, ss2772977414, ss2989438055, ss3344210989, ss3628056112, ss3631577049, ss3636450881 NC_000002.11:48018080:A>G NC_000002.12:47790941:A>G (self)
RCV000030265.4, RCV000035321.10, RCV000162362.1, RCV000616289.1, 192129474, ss472343121, ss538293019, ss2229920160, ss3024038476, ss3306786969 NC_000002.12:47790941:A>G NC_000002.12:47790941:A>G (self)
ss2421091, ss2924021, ss4384536, ss24636615, ss28497392, ss28512071, ss37042835, ss48411758, ss68813168, ss76862477, ss81586979, ss86344850, ss159701918, ss160462944 NT_022184.15:26839967:A>G NC_000002.12:47790941: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.

12 citations for rs1800932
PMID Title Author Year Journal
10537275 Germ-line msh6 mutations in colorectal cancer families. Kolodner RD et al. 1999 Cancer research
15805151 No MSH6 germline mutations in breast cancer families with colorectal and/or endometrial cancer. Vahteristo P et al. 2005 Journal of medical genetics
20149637 Common variants in human CRC genes as low-risk alleles. Picelli S et al. 2010 European journal of cancer (Oxford, England
20386703 Association between DNA damage response and repair genes and risk of invasive serous ovarian cancer. Schildkraut JM et al. 2010 PloS one
23565320 DNA repair genotype and lung cancer risk in the beta-carotene and retinol efficacy trial. Doherty JA et al. 2013 International journal of molecular epidemiology and genetics
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics
24357391 DNA mismatch repair gene MSH6 implicated in determining age at natural menopause. Perry JR et al. 2014 Human molecular genetics
24689082 A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes. Hansen MF et al. 2014 Molecular genetics & genomic medicine
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
25938433 A study of molecular signals deregulating mismatch repair genes in prostate cancer compared to benign prostatic hyperplasia. Basu S et al. 2015 PloS one
26739522 Impact of DNA mismatch repair system alterations on human fertility and related treatments. Hu MH et al. 2016 Journal of Zhejiang University. Science. B

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: 0.1.4.post833+d3ba21e