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dbSNP Short Genetic Variations

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.

rs6151616

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr5:80665651 (GRCh38.p12) 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=0.11861 (14894/125568, TOPMED)
C=0.1112 (3438/30926, GnomAD)
C=0.088 (441/5008, 1000G) (+ 3 more)
C=0.106 (477/4480, Estonian)
C=0.178 (686/3854, ALSPAC)
C=0.163 (606/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MSH3 : Intron 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.p12 chr 5 NC_000005.10:g.80665651T>C
GRCh37.p13 chr 5 NC_000005.9:g.79961470T>C
MSH3 RefSeqGene NG_016607.1:g.16177T>C
Gene: MSH3, mutS homolog 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MSH3 transcript NM_002439.4:c. 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.

Not Reported in ClinVar
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
TopMed Global Study-wide 125568 T=0.88139 C=0.11861
gnomAD - Genomes Global Study-wide 30926 T=0.8888 C=0.1112
gnomAD - Genomes European Sub 18468 T=0.8562 C=0.1438
gnomAD - Genomes African Sub 8720 T=0.939 C=0.061
gnomAD - Genomes East Asian Sub 1620 T=1.000 C=0.000
gnomAD - Genomes Other Sub 978 T=0.88 C=0.12
gnomAD - Genomes American Sub 838 T=0.92 C=0.08
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.80 C=0.20
1000Genomes Global Study-wide 5008 T=0.912 C=0.088
1000Genomes African Sub 1322 T=0.952 C=0.048
1000Genomes East Asian Sub 1008 T=1.000 C=0.000
1000Genomes Europe Sub 1006 T=0.848 C=0.152
1000Genomes South Asian Sub 978 T=0.85 C=0.15
1000Genomes American Sub 694 T=0.88 C=0.12
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.894 C=0.106
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.822 C=0.178
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.837 C=0.163
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 Note
GRCh38.p12 chr 5 NC_000005.10:g.80665651T= NC_000005.10:g.80665651T>C
GRCh37.p13 chr 5 NC_000005.9:g.79961470T= NC_000005.9:g.79961470T>C
MSH3 RefSeqGene NG_016607.1:g.16177T= NG_016607.1:g.16177T>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#.

50 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss8485282 Apr 21, 2003 (114)
2 ILLUMINA ss67447351 Dec 01, 2006 (127)
3 ILLUMINA ss67798527 Dec 01, 2006 (127)
4 ILLUMINA ss68249588 Dec 12, 2006 (127)
5 ILLUMINA ss70860775 May 24, 2008 (130)
6 ILLUMINA ss71448026 May 17, 2007 (127)
7 ILLUMINA ss75565609 Dec 07, 2007 (129)
8 CGM_KYOTO ss76862413 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss84471605 Dec 15, 2007 (130)
10 ILLUMINA ss154355734 Dec 01, 2009 (131)
11 ILLUMINA ss159532009 Dec 01, 2009 (131)
12 ILLUMINA ss173988884 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss206764675 Jul 04, 2010 (132)
14 1000GENOMES ss221768017 Jul 14, 2010 (132)
15 1000GENOMES ss233009916 Jul 14, 2010 (132)
16 GMI ss285205314 Apr 25, 2013 (138)
17 PJP ss293389061 May 09, 2011 (134)
18 ILLUMINA ss537342824 Sep 08, 2015 (146)
19 SSMP ss652370178 Apr 25, 2013 (138)
20 ILLUMINA ss833043250 Aug 21, 2014 (142)
21 ILLUMINA ss833634078 Aug 21, 2014 (142)
22 EVA-GONL ss981740021 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1072759010 Aug 21, 2014 (142)
24 1000GENOMES ss1315756715 Aug 21, 2014 (142)
25 DDI ss1430395432 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1581205139 Apr 01, 2015 (144)
27 EVA_DECODE ss1591258869 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1613236965 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1656230998 Apr 01, 2015 (144)
30 EVA_SVP ss1712776461 Apr 01, 2015 (144)
31 HAMMER_LAB ss1803742135 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1924995730 Feb 12, 2016 (147)
33 JJLAB ss2023104582 Sep 14, 2016 (149)
34 USC_VALOUEV ss2151260354 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2275065627 Dec 20, 2016 (150)
36 TOPMED ss2443302629 Dec 20, 2016 (150)
37 GRF ss2706811661 Nov 08, 2017 (151)
38 GNOMAD ss2826544204 Nov 08, 2017 (151)
39 AFFY ss2985956899 Nov 08, 2017 (151)
40 SWEGEN ss2997207889 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3025337233 Nov 08, 2017 (151)
42 CSHL ss3346463661 Nov 08, 2017 (151)
43 TOPMED ss3468922896 Nov 08, 2017 (151)
44 ILLUMINA ss3629270134 Oct 12, 2018 (152)
45 ILLUMINA ss3638562795 Oct 12, 2018 (152)
46 ILLUMINA ss3639284047 Oct 12, 2018 (152)
47 ILLUMINA ss3639939397 Oct 12, 2018 (152)
48 ILLUMINA ss3643508091 Oct 12, 2018 (152)
49 ILLUMINA ss3643984895 Oct 12, 2018 (152)
50 URBANLAB ss3648099688 Oct 12, 2018 (152)
51 1000Genomes NC_000005.9 - 79961470 Oct 12, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 79961470 Oct 12, 2018 (152)
53 Genetic variation in the Estonian population NC_000005.9 - 79961470 Oct 12, 2018 (152)
54 gnomAD - Genomes NC_000005.9 - 79961470 Oct 12, 2018 (152)
55 TopMed NC_000005.10 - 80665651 Oct 12, 2018 (152)
56 UK 10K study - Twins NC_000005.9 - 79961470 Oct 12, 2018 (152)
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)
rs58502753 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss206764675, ss285205314, ss293389061, ss1591258869, ss1712776461, ss3639284047, ss3639939397, ss3643508091, ss3643984895 NC_000005.8:79997225:T= NC_000005.10:80665650:T= (self)
27381377, 15223821, 10825165, 167171960, 15223821, ss221768017, ss233009916, ss537342824, ss652370178, ss833043250, ss833634078, ss981740021, ss1072759010, ss1315756715, ss1430395432, ss1581205139, ss1613236965, ss1656230998, ss1803742135, ss1924995730, ss2023104582, ss2151260354, ss2443302629, ss2706811661, ss2826544204, ss2985956899, ss2997207889, ss3346463661, ss3629270134, ss3638562795 NC_000005.9:79961469:T= NC_000005.10:80665650:T= (self)
314553651, ss2275065627, ss3025337233, ss3468922896, ss3648099688 NC_000005.10:80665650:T= NC_000005.10:80665650:T= (self)
ss8485282, ss67447351, ss67798527, ss68249588, ss70860775, ss71448026, ss75565609, ss76862413, ss84471605, ss154355734, ss159532009, ss173988884 NT_006713.15:30555828:T= NC_000005.10:80665650:T= (self)
ss206764675, ss285205314, ss293389061, ss1591258869, ss1712776461, ss3639284047, ss3639939397, ss3643508091, ss3643984895 NC_000005.8:79997225:T>C NC_000005.10:80665650:T>C (self)
27381377, 15223821, 10825165, 167171960, 15223821, ss221768017, ss233009916, ss537342824, ss652370178, ss833043250, ss833634078, ss981740021, ss1072759010, ss1315756715, ss1430395432, ss1581205139, ss1613236965, ss1656230998, ss1803742135, ss1924995730, ss2023104582, ss2151260354, ss2443302629, ss2706811661, ss2826544204, ss2985956899, ss2997207889, ss3346463661, ss3629270134, ss3638562795 NC_000005.9:79961469:T>C NC_000005.10:80665650:T>C (self)
314553651, ss2275065627, ss3025337233, ss3468922896, ss3648099688 NC_000005.10:80665650:T>C NC_000005.10:80665650:T>C (self)
ss8485282, ss67447351, ss67798527, ss68249588, ss70860775, ss71448026, ss75565609, ss76862413, ss84471605, ss154355734, ss159532009, ss173988884 NT_006713.15:30555828:T>C NC_000005.10:80665650: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 rs6151616

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.post63+3f7b20b