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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.

rs10822050

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr10:62679011 (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=0.33806 (42450/125568, TOPMED)
C=0.3459 (10838/31334, GnomAD)
C=0.336 (1685/5008, 1000G) (+ 5 more)
C=0.385 (1724/4480, Estonian)
C=0.383 (1475/3854, ALSPAC)
C=0.386 (1431/3708, TWINSUK)
C=0.40 (241/600, NorthernSweden)
T=0.48 (102/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 10 NC_000010.11:g.62679011T>C
GRCh37.p13 chr 10 NC_000010.10:g.64438771T>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

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=0.66194 C=0.33806
gnomAD - Genomes Global Study-wide 31334 T=0.6541 C=0.3459
gnomAD - Genomes European Sub 18860 T=0.6113 C=0.3887
gnomAD - Genomes African Sub 8698 T=0.783 C=0.217
gnomAD - Genomes East Asian Sub 1552 T=0.428 C=0.572
gnomAD - Genomes Other Sub 1088 T=0.641 C=0.359
gnomAD - Genomes American Sub 846 T=0.74 C=0.26
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.58 C=0.42
1000Genomes Global Study-wide 5008 T=0.664 C=0.336
1000Genomes African Sub 1322 T=0.812 C=0.188
1000Genomes East Asian Sub 1008 T=0.463 C=0.537
1000Genomes Europe Sub 1006 T=0.623 C=0.377
1000Genomes South Asian Sub 978 T=0.65 C=0.35
1000Genomes American Sub 694 T=0.75 C=0.25
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.615 C=0.385
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.617 C=0.383
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.614 C=0.386
Northern Sweden ACPOP Study-wide 600 T=0.60 C=0.40
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.48 C=0.52
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 10 NC_000010.11:g.62679011= NC_000010.11:g.62679011T>C
GRCh37.p13 chr 10 NC_000010.10:g.64438771= NC_000010.10:g.64438771T>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#.

54 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss16048880 Feb 27, 2004 (120)
2 SC_SNP ss18452618 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19901275 Feb 27, 2004 (120)
4 SSAHASNP ss20732313 Apr 05, 2004 (121)
5 ABI ss39793575 Mar 13, 2006 (126)
6 HGSV ss83175161 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss88240271 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss97561098 Feb 05, 2009 (130)
9 BGI ss102884671 Dec 01, 2009 (131)
10 1000GENOMES ss109499848 Jan 24, 2009 (130)
11 1000GENOMES ss113363536 Jan 25, 2009 (130)
12 ILLUMINA-UK ss119194765 Feb 15, 2009 (130)
13 ENSEMBL ss131909265 Dec 01, 2009 (131)
14 ENSEMBL ss137960055 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss168463955 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss170203610 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss174582455 Jul 04, 2010 (132)
18 BUSHMAN ss201609460 Jul 04, 2010 (132)
19 1000GENOMES ss224765478 Jul 14, 2010 (132)
20 1000GENOMES ss235204517 Jul 15, 2010 (132)
21 1000GENOMES ss241904682 Jul 15, 2010 (132)
22 BL ss254368478 May 09, 2011 (134)
23 GMI ss280645414 May 04, 2012 (137)
24 PJP ss290853249 May 09, 2011 (134)
25 TISHKOFF ss562000986 Apr 25, 2013 (138)
26 SSMP ss656838141 Apr 25, 2013 (138)
27 EVA-GONL ss987564166 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1077042877 Aug 21, 2014 (142)
29 1000GENOMES ss1337721757 Aug 21, 2014 (142)
30 DDI ss1426343132 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1575161503 Apr 01, 2015 (144)
32 EVA_DECODE ss1597231887 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1624716964 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1667710997 Apr 01, 2015 (144)
35 HAMMER_LAB ss1806421362 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1930927403 Feb 12, 2016 (147)
37 GENOMED ss1967145989 Jul 19, 2016 (147)
38 JJLAB ss2026187406 Sep 14, 2016 (149)
39 USC_VALOUEV ss2154460378 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2175331072 Dec 20, 2016 (150)
41 TOPMED ss2338364336 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2627563037 Nov 08, 2017 (151)
43 GRF ss2698704757 Nov 08, 2017 (151)
44 GNOMAD ss2889580537 Nov 08, 2017 (151)
45 SWEGEN ss3006594631 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3026884598 Nov 08, 2017 (151)
47 TOPMED ss3121683128 Nov 08, 2017 (151)
48 CSHL ss3349155994 Nov 08, 2017 (151)
49 URBANLAB ss3649388698 Oct 12, 2018 (152)
50 EGCUT_WGS ss3674008497 Jul 13, 2019 (153)
51 EVA_DECODE ss3690018522 Jul 13, 2019 (153)
52 ACPOP ss3737384781 Jul 13, 2019 (153)
53 EVA ss3748188166 Jul 13, 2019 (153)
54 KHV_HUMAN_GENOMES ss3813562940 Jul 13, 2019 (153)
55 1000Genomes NC_000010.10 - 64438771 Oct 12, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 64438771 Oct 12, 2018 (152)
57 Genetic variation in the Estonian population NC_000010.10 - 64438771 Oct 12, 2018 (152)
58 gnomAD - Genomes NC_000010.10 - 64438771 Jul 13, 2019 (153)
59 Northern Sweden NC_000010.10 - 64438771 Jul 13, 2019 (153)
60 TopMed NC_000010.11 - 62679011 Oct 12, 2018 (152)
61 UK 10K study - Twins NC_000010.10 - 64438771 Oct 12, 2018 (152)
62 A Vietnamese Genetic Variation Database NC_000010.10 - 64438771 Jul 13, 2019 (153)
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)
rs59492940 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83175161 NC_000010.8:64108776:T:C NC_000010.11:62679010:T:C (self)
ss88240271, ss109499848, ss113363536, ss119194765, ss168463955, ss170203610, ss174582455, ss201609460, ss254368478, ss280645414, ss290853249, ss1597231887 NC_000010.9:64108776:T:C NC_000010.11:62679010:T:C (self)
50119815, 27818764, 19746745, 136948201, 10669646, 27818764, 6178140, ss224765478, ss235204517, ss241904682, ss562000986, ss656838141, ss987564166, ss1077042877, ss1337721757, ss1426343132, ss1575161503, ss1624716964, ss1667710997, ss1806421362, ss1930927403, ss1967145989, ss2026187406, ss2154460378, ss2338364336, ss2627563037, ss2698704757, ss2889580537, ss3006594631, ss3349155994, ss3674008497, ss3737384781, ss3748188166 NC_000010.10:64438770:T:C NC_000010.11:62679010:T:C (self)
44251139, ss2175331072, ss3026884598, ss3121683128, ss3649388698, ss3690018522, ss3813562940 NC_000010.11:62679010:T:C NC_000010.11:62679010:T:C (self)
ss16048880, ss18452618, ss19901275, ss20732313 NT_008583.16:12989925:T:C NC_000010.11:62679010:T:C (self)
ss39793575, ss97561098, ss102884671, ss131909265, ss137960055 NT_030059.13:15243234:T:C NC_000010.11:62679010: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 rs10822050

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.post246+3cda961