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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.

rs373418713

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:47800139 (GRCh38.p13) 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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000008 (1/121158, ExAC)
G=0.00004 (1/23038, ALFA)
T=0.00015 (2/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MSH6 : Missense Variant
Publications
0 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.p13 chr 2 NC_000002.12:g.47800139C>G
GRCh38.p13 chr 2 NC_000002.12:g.47800139C>T
GRCh37.p13 chr 2 NC_000002.11:g.48027278C>G
GRCh37.p13 chr 2 NC_000002.11:g.48027278C>T
MSH6 RefSeqGene (LRG_219) NG_007111.1:g.21993C>G
MSH6 RefSeqGene (LRG_219) NG_007111.1:g.21993C>T
Gene: MSH6, mutS homolog 6 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MSH6 transcript variant 1 NM_000179.3:c.2156C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 1 NP_000170.1:p.Thr719Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant 1 NM_000179.3:c.2156C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 1 NP_000170.1:p.Thr719Ile T (Thr) > I (Ile) Missense Variant
MSH6 transcript variant 4 NM_001281494.2:c.1250C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 3 NP_001268423.1:p.Thr417Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant 4 NM_001281494.2:c.1250C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 3 NP_001268423.1:p.Thr417Ile T (Thr) > I (Ile) Missense Variant
MSH6 transcript variant 3 NM_001281493.2:c.1250C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 3 NP_001268422.1:p.Thr417Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant 3 NM_001281493.2:c.1250C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 3 NP_001268422.1:p.Thr417Ile T (Thr) > I (Ile) Missense Variant
MSH6 transcript variant 2 NM_001281492.2:c.1766C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 2 NP_001268421.1:p.Thr589Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant 2 NM_001281492.2:c.1766C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 2 NP_001268421.1:p.Thr589Ile T (Thr) > I (Ile) Missense Variant
MSH6 transcript variant X1 XM_024452819.1:c.2156C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X1 XP_024308587.1:p.Thr719Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant X1 XM_024452819.1:c.2156C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X1 XP_024308587.1:p.Thr719Ile T (Thr) > I (Ile) Missense Variant
MSH6 transcript variant X2 XM_024452820.1:c.1973C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X2 XP_024308588.1:p.Thr658Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant X2 XM_024452820.1:c.1973C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X2 XP_024308588.1:p.Thr658Ile T (Thr) > I (Ile) Missense Variant
MSH6 transcript variant X3 XM_024452821.1:c.1859C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X3 XP_024308589.1:p.Thr620Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant X3 XM_024452821.1:c.1859C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X3 XP_024308589.1:p.Thr620Ile T (Thr) > I (Ile) Missense Variant
MSH6 transcript variant X4 XM_024452822.1:c.1250C>G T [ACT] > S [AGT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X4 XP_024308590.1:p.Thr417Ser T (Thr) > S (Ser) Missense Variant
MSH6 transcript variant X4 XM_024452822.1:c.1250C>T T [ACT] > I [ATT] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X4 XP_024308590.1:p.Thr417Ile T (Thr) > I (Ile) Missense 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: 630273 )
ClinVar Accession Disease Names Clinical Significance
RCV000806588.1 Hereditary nonpolyposis colorectal neoplasms Uncertain-Significance
Allele: T (allele ID: 221281 )
ClinVar Accession Disease Names Clinical Significance
RCV000205525.7 Hereditary nonpolyposis colorectal neoplasms Uncertain-Significance
RCV000214718.4 Hereditary cancer-predisposing syndrome Uncertain-Significance
RCV000985830.1 not provided Uncertain-Significance

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 23038 C=0.99996 G=0.00004, T=0.00000
European Sub 15752 C=0.99994 G=0.00006, T=0.00000
African Sub 3492 C=1.0000 G=0.0000, T=0.0000
African Others Sub 122 C=1.000 G=0.000, T=0.000
African American Sub 3370 C=1.0000 G=0.0000, T=0.0000
Asian Sub 168 C=1.000 G=0.000, T=0.000
East Asian Sub 112 C=1.000 G=0.000, T=0.000
Other Asian Sub 56 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
South Asian Sub 98 C=1.00 G=0.00, T=0.00
Other Sub 2772 C=1.0000 G=0.0000, T=0.0000


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
ExAC Global Study-wide 121158 C=0.999992 T=0.000008
ExAC Europe Sub 73210 C=0.99999 T=0.00001
ExAC Asian Sub 25144 C=1.00000 T=0.00000
ExAC American Sub 11558 C=1.00000 T=0.00000
ExAC African Sub 10342 C=1.00000 T=0.00000
ExAC Other Sub 904 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99985 T=0.00015
GO Exome Sequencing Project European American Sub 8600 C=0.9998 T=0.0002
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
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 C= G T
GRCh38.p13 chr 2 NC_000002.12:g.47800139= NC_000002.12:g.47800139C>G NC_000002.12:g.47800139C>T
GRCh37.p13 chr 2 NC_000002.11:g.48027278= NC_000002.11:g.48027278C>G NC_000002.11:g.48027278C>T
MSH6 RefSeqGene (LRG_219) NG_007111.1:g.21993= NG_007111.1:g.21993C>G NG_007111.1:g.21993C>T
MSH6 transcript variant 1 NM_000179.3:c.2156= NM_000179.3:c.2156C>G NM_000179.3:c.2156C>T
MSH6 transcript variant 1 NM_000179.2:c.2156= NM_000179.2:c.2156C>G NM_000179.2:c.2156C>T
MSH6 transcript variant 3 NM_001281493.2:c.1250= NM_001281493.2:c.1250C>G NM_001281493.2:c.1250C>T
MSH6 transcript variant 3 NM_001281493.1:c.1250= NM_001281493.1:c.1250C>G NM_001281493.1:c.1250C>T
MSH6 transcript variant 4 NM_001281494.2:c.1250= NM_001281494.2:c.1250C>G NM_001281494.2:c.1250C>T
MSH6 transcript variant 4 NM_001281494.1:c.1250= NM_001281494.1:c.1250C>G NM_001281494.1:c.1250C>T
MSH6 transcript variant 2 NM_001281492.2:c.1766= NM_001281492.2:c.1766C>G NM_001281492.2:c.1766C>T
MSH6 transcript variant 2 NM_001281492.1:c.1766= NM_001281492.1:c.1766C>G NM_001281492.1:c.1766C>T
MSH6 transcript variant X1 XM_024452819.1:c.2156= XM_024452819.1:c.2156C>G XM_024452819.1:c.2156C>T
MSH6 transcript variant X3 XM_024452821.1:c.1859= XM_024452821.1:c.1859C>G XM_024452821.1:c.1859C>T
MSH6 transcript variant X4 XM_024452822.1:c.1250= XM_024452822.1:c.1250C>G XM_024452822.1:c.1250C>T
MSH6 transcript variant X2 XM_024452820.1:c.1973= XM_024452820.1:c.1973C>G XM_024452820.1:c.1973C>T
DNA mismatch repair protein Msh6 isoform 1 NP_000170.1:p.Thr719= NP_000170.1:p.Thr719Ser NP_000170.1:p.Thr719Ile
DNA mismatch repair protein Msh6 isoform 3 NP_001268422.1:p.Thr417= NP_001268422.1:p.Thr417Ser NP_001268422.1:p.Thr417Ile
DNA mismatch repair protein Msh6 isoform 3 NP_001268423.1:p.Thr417= NP_001268423.1:p.Thr417Ser NP_001268423.1:p.Thr417Ile
DNA mismatch repair protein Msh6 isoform 2 NP_001268421.1:p.Thr589= NP_001268421.1:p.Thr589Ser NP_001268421.1:p.Thr589Ile
DNA mismatch repair protein Msh6 isoform X1 XP_024308587.1:p.Thr719= XP_024308587.1:p.Thr719Ser XP_024308587.1:p.Thr719Ile
DNA mismatch repair protein Msh6 isoform X3 XP_024308589.1:p.Thr620= XP_024308589.1:p.Thr620Ser XP_024308589.1:p.Thr620Ile
DNA mismatch repair protein Msh6 isoform X4 XP_024308590.1:p.Thr417= XP_024308590.1:p.Thr417Ser XP_024308590.1:p.Thr417Ile
DNA mismatch repair protein Msh6 isoform X2 XP_024308588.1:p.Thr658= XP_024308588.1:p.Thr658Ser XP_024308588.1:p.Thr658Ile
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#.

10 SubSNP, 9 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712416087 Apr 25, 2013 (138)
2 EVA_EXAC ss1686300967 Apr 01, 2015 (144)
3 GNOMAD ss2732654202 Nov 08, 2017 (151)
4 GNOMAD ss2746677003 Nov 08, 2017 (151)
5 GNOMAD ss2772978349 Nov 08, 2017 (151)
6 TOPMED ss3306789285 Nov 08, 2017 (151)
7 TOPMED ss3306789286 Nov 08, 2017 (151)
8 EVA ss3823768021 Apr 25, 2020 (154)
9 TOPMED ss4504135770 Apr 26, 2021 (155)
10 TOPMED ss4504135771 Apr 26, 2021 (155)
11 ExAC NC_000002.11 - 48027278 Oct 11, 2018 (152)
12 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 56800029 (NC_000002.12:47800138:C:G 1/140200)
Row 56800030 (NC_000002.12:47800138:C:T 4/140200)

- Apr 26, 2021 (155)
13 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 56800029 (NC_000002.12:47800138:C:G 1/140200)
Row 56800030 (NC_000002.12:47800138:C:T 4/140200)

- Apr 26, 2021 (155)
14 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 1702660 (NC_000002.11:48027277:C:C 250933/250934, NC_000002.11:48027277:C:G 1/250934)
Row 1702661 (NC_000002.11:48027277:C:C 250933/250934, NC_000002.11:48027277:C:T 1/250934)

- Jul 13, 2019 (153)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 1702660 (NC_000002.11:48027277:C:C 250933/250934, NC_000002.11:48027277:C:G 1/250934)
Row 1702661 (NC_000002.11:48027277:C:C 250933/250934, NC_000002.11:48027277:C:T 1/250934)

- Jul 13, 2019 (153)
16 GO Exome Sequencing Project NC_000002.11 - 48027278 Oct 11, 2018 (152)
17 TopMed

Submission ignored due to conflicting rows:
Row 307958649 (NC_000002.12:47800138:C:G 1/264690)
Row 307958650 (NC_000002.12:47800138:C:T 2/264690)

- Apr 26, 2021 (155)
18 TopMed

Submission ignored due to conflicting rows:
Row 307958649 (NC_000002.12:47800138:C:G 1/264690)
Row 307958650 (NC_000002.12:47800138:C:T 2/264690)

- Apr 26, 2021 (155)
19 ALFA NC_000002.12 - 47800139 Apr 26, 2021 (155)
20 ClinVar RCV000205525.7 Apr 26, 2021 (155)
21 ClinVar RCV000214718.4 Apr 26, 2021 (155)
22 ClinVar RCV000806588.1 Apr 25, 2020 (154)
23 ClinVar RCV000985830.1 Apr 25, 2020 (154)
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
ss2732654202 NC_000002.11:48027277:C:G NC_000002.12:47800138:C:G (self)
RCV000806588.1, 192131266, 4157571473, ss3306789285, ss4504135770 NC_000002.12:47800138:C:G NC_000002.12:47800138:C:G (self)
6170673, 226485, ss712416087, ss1686300967, ss2732654202, ss2746677003, ss2772978349, ss3823768021 NC_000002.11:48027277:C:T NC_000002.12:47800138:C:T (self)
RCV000205525.7, RCV000214718.4, RCV000985830.1, 192131266, 4157571473, ss3306789286, ss4504135771 NC_000002.12:47800138:C:T NC_000002.12:47800138:C:T (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 rs373418713

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.post596+ae089ad