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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.


Current Build 152

Released October 2, 2018

Homo sapiens
chr5:175751872 (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.

Variation Type
SNV Single Nucleotide Variation
G=0.04727 (5936/125568, TOPMED)
G=0.0422 (1307/30954, GnomAD)
G=0.054 (271/5008, 1000G) (+ 3 more)
G=0.019 (87/4480, Estonian)
G=0.017 (65/3854, ALSPAC)
G=0.015 (55/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
0 citations
Genomic View
See rs on genome

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.175751872A>G
GRCh37.p13 chr 5 NC_000005.9:g.175178875A>G

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

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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.95273 G=0.04727
gnomAD - Genomes Global Study-wide 30954 A=0.9578 G=0.0422
gnomAD - Genomes European Sub 18500 A=0.9841 G=0.0159
gnomAD - Genomes African Sub 8714 A=0.893 G=0.107
gnomAD - Genomes East Asian Sub 1620 A=0.973 G=0.027
gnomAD - Genomes Other Sub 980 A=0.98 G=0.02
gnomAD - Genomes American Sub 838 A=0.99 G=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 302 A=0.97 G=0.03
1000Genomes Global Study-wide 5008 A=0.946 G=0.054
1000Genomes African Sub 1322 A=0.880 G=0.120
1000Genomes East Asian Sub 1008 A=0.961 G=0.039
1000Genomes Europe Sub 1006 A=0.979 G=0.021
1000Genomes South Asian Sub 978 A=0.95 G=0.05
1000Genomes American Sub 694 A=0.99 G=0.01
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.981 G=0.019
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.983 G=0.017
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.985 G=0.015

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.p12 chr 5 NC_000005.10:g.175751872A= NC_000005.10:g.17575187...


GRCh37.p13 chr 5 NC_000005.9:g.175178875A= NC_000005.9:g.175178875A>G

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#.

35 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13886938 Dec 05, 2003 (119)
2 AFFY ss76432808 Dec 07, 2007 (129)
3 HGSV ss82999215 Dec 15, 2007 (130)
4 KRIBB_YJKIM ss104997512 Feb 05, 2009 (130)
5 1000GENOMES ss113715406 Jan 25, 2009 (130)
6 ILLUMINA ss159854946 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss166315462 Jul 04, 2010 (132)
8 BUSHMAN ss201254085 Jul 04, 2010 (132)
9 1000GENOMES ss222137343 Jul 14, 2010 (132)
10 1000GENOMES ss233271265 Jul 14, 2010 (132)
11 1000GENOMES ss240368528 Jul 15, 2010 (132)
12 ILLUMINA ss479486337 Sep 08, 2015 (146)
13 ILLUMINA ss533959510 Sep 08, 2015 (146)
14 TISHKOFF ss558914435 Apr 25, 2013 (138)
15 SSMP ss652823594 Apr 25, 2013 (138)
16 EVA-GONL ss982448905 Aug 21, 2014 (142)
17 1000GENOMES ss1318466060 Aug 21, 2014 (142)
18 HAMMER_LAB ss1397437180 Sep 08, 2015 (146)
19 EVA_DECODE ss1591993188 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1614688657 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1657682690 Apr 01, 2015 (144)
22 EVA_SVP ss1712825119 Apr 01, 2015 (144)
23 WEILL_CORNELL_DGM ss1925699298 Feb 12, 2016 (147)
24 USC_VALOUEV ss2151624636 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2280784799 Dec 20, 2016 (150)
26 TOPMED ss2449112040 Dec 20, 2016 (150)
27 GRF ss2707202887 Nov 08, 2017 (151)
28 GNOMAD ss2834339185 Nov 08, 2017 (151)
29 AFFY ss2985977836 Nov 08, 2017 (151)
30 SWEGEN ss2998295105 Nov 08, 2017 (151)
31 ILLUMINA ss3022559878 Nov 08, 2017 (151)
32 TOPMED ss3486847262 Nov 08, 2017 (151)
33 ILLUMINA ss3629412587 Oct 12, 2018 (152)
34 ILLUMINA ss3636751584 Oct 12, 2018 (152)
35 ILLUMINA ss3653066966 Oct 12, 2018 (152)
36 1000Genomes NC_000005.9 - 175178875 Oct 12, 2018 (152)
37 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 175178875 Oct 12, 2018 (152)
38 Genetic variation in the Estonian population NC_000005.9 - 175178875 Oct 12, 2018 (152)
39 gnomAD - Genomes NC_000005.9 - 175178875 Oct 12, 2018 (152)
40 TopMed NC_000005.10 - 175751872 Oct 12, 2018 (152)
41 UK 10K study - Twins NC_000005.9 - 175178875 Oct 12, 2018 (152)

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)
rs58929378 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss76432808, ss82999215, ss113715406, ss166315462, ss201254085, ss1397437180, ss1591993188, ss1712825119 NC_000005.8:175111480:A:G NC_000005.10:175751871:A:G (self)
30188809, 16812151, 11972588, 174966941, 16812151, ss222137343, ss233271265, ss240368528, ss479486337, ss533959510, ss558914435, ss652823594, ss982448905, ss1318466060, ss1614688657, ss1657682690, ss1925699298, ss2151624636, ss2449112040, ss2707202887, ss2834339185, ss2985977836, ss2998295105, ss3022559878, ss3629412587, ss3636751584, ss3653066966 NC_000005.9:175178874:A:G NC_000005.10:175751871:A:G (self)
329514975, ss2280784799, ss3486847262 NC_000005.10:175751871:A:G NC_000005.10:175751871:A:G (self)
ss13886938 NT_023133.11:19988460:A:G NC_000005.10:175751871:A:G (self)
ss104997512, ss159854946 NT_023133.13:19990147:A:G NC_000005.10:175751871:A:G (self)

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

No publications for rs10039217

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.post104+4a6ee9c