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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.

rs362554

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:10320313 (GRCh38.p14) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.081473 (21565/264690, TOPMED)
T=0.076898 (10778/140160, GnomAD)
T=0.21810 (6163/28258, 14KJPN) (+ 18 more)
T=0.07104 (1342/18890, ALFA)
T=0.21969 (3682/16760, 8.3KJPN)
T=0.1038 (665/6404, 1000G_30x)
T=0.1078 (540/5008, 1000G)
T=0.0721 (323/4480, Estonian)
T=0.0524 (202/3854, ALSPAC)
T=0.0593 (220/3708, TWINSUK)
T=0.2427 (711/2930, KOREAN)
T=0.2303 (422/1832, Korea1K)
T=0.048 (48/998, GoNL)
T=0.038 (23/600, NorthernSweden)
T=0.037 (8/216, Qatari)
T=0.307 (65/212, Vietnamese)
T=0.042 (5/120, HapMap)
C=0.429 (48/112, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.92896 T=0.07104
European Sub 14286 C=0.94029 T=0.05971
African Sub 2946 C=0.8829 T=0.1171
African Others Sub 114 C=0.860 T=0.140
African American Sub 2832 C=0.8838 T=0.1162
Asian Sub 112 C=0.768 T=0.232
East Asian Sub 86 C=0.77 T=0.23
Other Asian Sub 26 C=0.77 T=0.23
Latin American 1 Sub 146 C=0.966 T=0.034
Latin American 2 Sub 610 C=0.915 T=0.085
South Asian Sub 98 C=0.91 T=0.09
Other Sub 692 C=0.925 T=0.075


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
TopMed Global Study-wide 264690 C=0.918527 T=0.081473
gnomAD - Genomes Global Study-wide 140160 C=0.923102 T=0.076898
gnomAD - Genomes European Sub 75916 C=0.94620 T=0.05380
gnomAD - Genomes African Sub 41998 C=0.88649 T=0.11351
gnomAD - Genomes American Sub 13650 C=0.93121 T=0.06879
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9889 T=0.0111
gnomAD - Genomes East Asian Sub 3122 C=0.7431 T=0.2569
gnomAD - Genomes Other Sub 2150 C=0.9307 T=0.0693
14KJPN JAPANESE Study-wide 28258 C=0.78190 T=0.21810
Allele Frequency Aggregator Total Global 18890 C=0.92896 T=0.07104
Allele Frequency Aggregator European Sub 14286 C=0.94029 T=0.05971
Allele Frequency Aggregator African Sub 2946 C=0.8829 T=0.1171
Allele Frequency Aggregator Other Sub 692 C=0.925 T=0.075
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.915 T=0.085
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.966 T=0.034
Allele Frequency Aggregator Asian Sub 112 C=0.768 T=0.232
Allele Frequency Aggregator South Asian Sub 98 C=0.91 T=0.09
8.3KJPN JAPANESE Study-wide 16760 C=0.78031 T=0.21969
1000Genomes_30x Global Study-wide 6404 C=0.8962 T=0.1038
1000Genomes_30x African Sub 1786 C=0.8875 T=0.1125
1000Genomes_30x Europe Sub 1266 C=0.9589 T=0.0411
1000Genomes_30x South Asian Sub 1202 C=0.9709 T=0.0291
1000Genomes_30x East Asian Sub 1170 C=0.7436 T=0.2564
1000Genomes_30x American Sub 980 C=0.921 T=0.079
1000Genomes Global Study-wide 5008 C=0.8922 T=0.1078
1000Genomes African Sub 1322 C=0.8850 T=0.1150
1000Genomes East Asian Sub 1008 C=0.7450 T=0.2550
1000Genomes Europe Sub 1006 C=0.9563 T=0.0437
1000Genomes South Asian Sub 978 C=0.970 T=0.030
1000Genomes American Sub 694 C=0.916 T=0.084
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9279 T=0.0721
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9476 T=0.0524
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9407 T=0.0593
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.7573 T=0.2427
Korean Genome Project KOREAN Study-wide 1832 C=0.7697 T=0.2303
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.952 T=0.048
Northern Sweden ACPOP Study-wide 600 C=0.962 T=0.038
Qatari Global Study-wide 216 C=0.963 T=0.037
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.693 T=0.307
HapMap Global Study-wide 120 C=0.958 T=0.042
HapMap American Sub 120 C=0.958 T=0.042
SGDP_PRJ Global Study-wide 112 C=0.429 T=0.571
The Danish reference pan genome Danish Study-wide 40 C=0.95 T=0.05
Siberian Global Study-wide 6 C=0.5 T=0.5
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.p14 chr 20 NC_000020.11:g.10320313C>T
GRCh37.p13 chr 20 NC_000020.10:g.10300961C>T
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

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= T
GRCh38.p14 chr 20 NC_000020.11:g.10320313= NC_000020.11:g.10320313C>T
GRCh37.p13 chr 20 NC_000020.10:g.10300961= NC_000020.10:g.10300961C>T
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#.

53 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 ACEVAN ss460007 Jul 12, 2000 (79)
2 ACEVAN ss4254927 Jan 04, 2002 (102)
3 SC_SNP ss8464938 Apr 21, 2003 (114)
4 PERLEGEN ss24092329 Sep 20, 2004 (123)
5 HGSV ss85594364 Dec 14, 2007 (130)
6 1000GENOMES ss113082917 Jan 25, 2009 (130)
7 GMI ss156162149 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss169080429 Jul 04, 2010 (132)
9 1000GENOMES ss228256388 Jul 14, 2010 (132)
10 1000GENOMES ss237762468 Jul 15, 2010 (132)
11 1000GENOMES ss243949045 Jul 15, 2010 (132)
12 GMI ss283299831 May 04, 2012 (137)
13 TISHKOFF ss566135582 Apr 25, 2013 (138)
14 SSMP ss662006565 Apr 25, 2013 (138)
15 EVA-GONL ss994538527 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1082072960 Aug 21, 2014 (142)
17 1000GENOMES ss1364063517 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1579436893 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1638411713 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1681405746 Apr 01, 2015 (144)
21 EVA_DECODE ss1698594482 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1938048986 Feb 12, 2016 (147)
23 GENOMED ss1969090798 Jul 19, 2016 (147)
24 JJLAB ss2029803728 Sep 14, 2016 (149)
25 USC_VALOUEV ss2158357467 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2241324426 Dec 20, 2016 (150)
27 SYSTEMSBIOZJU ss2629398943 Nov 08, 2017 (151)
28 GRF ss2704030738 Nov 08, 2017 (151)
29 GNOMAD ss2965429322 Nov 08, 2017 (151)
30 SWEGEN ss3017867341 Nov 08, 2017 (151)
31 BIOINF_KMB_FNS_UNIBA ss3028734861 Nov 08, 2017 (151)
32 EGCUT_WGS ss3684584345 Jul 13, 2019 (153)
33 EVA_DECODE ss3706558965 Jul 13, 2019 (153)
34 ACPOP ss3743248564 Jul 13, 2019 (153)
35 EVA ss3758421232 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3821595026 Jul 13, 2019 (153)
37 EVA ss3835587776 Apr 27, 2020 (154)
38 SGDP_PRJ ss3888731744 Apr 27, 2020 (154)
39 KRGDB ss3938920538 Apr 27, 2020 (154)
40 KOGIC ss3981822428 Apr 27, 2020 (154)
41 TOPMED ss5082253660 Apr 27, 2021 (155)
42 TOMMO_GENOMICS ss5228839159 Apr 27, 2021 (155)
43 1000G_HIGH_COVERAGE ss5308084772 Oct 13, 2022 (156)
44 EVA ss5436259275 Oct 13, 2022 (156)
45 HUGCELL_USP ss5500485384 Oct 13, 2022 (156)
46 1000G_HIGH_COVERAGE ss5614165441 Oct 13, 2022 (156)
47 SANFORD_IMAGENETICS ss5662864620 Oct 13, 2022 (156)
48 TOMMO_GENOMICS ss5787826920 Oct 13, 2022 (156)
49 YY_MCH ss5817815953 Oct 13, 2022 (156)
50 EVA ss5845443900 Oct 13, 2022 (156)
51 EVA ss5853068764 Oct 13, 2022 (156)
52 EVA ss5922673506 Oct 13, 2022 (156)
53 EVA ss5957766092 Oct 13, 2022 (156)
54 1000Genomes NC_000020.10 - 10300961 Oct 12, 2018 (152)
55 1000Genomes_30x NC_000020.11 - 10320313 Oct 13, 2022 (156)
56 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 10300961 Oct 12, 2018 (152)
57 Genetic variation in the Estonian population NC_000020.10 - 10300961 Oct 12, 2018 (152)
58 The Danish reference pan genome NC_000020.10 - 10300961 Apr 27, 2020 (154)
59 gnomAD - Genomes NC_000020.11 - 10320313 Apr 27, 2021 (155)
60 Genome of the Netherlands Release 5 NC_000020.10 - 10300961 Apr 27, 2020 (154)
61 HapMap NC_000020.11 - 10320313 Apr 27, 2020 (154)
62 KOREAN population from KRGDB NC_000020.10 - 10300961 Apr 27, 2020 (154)
63 Korean Genome Project NC_000020.11 - 10320313 Apr 27, 2020 (154)
64 Northern Sweden NC_000020.10 - 10300961 Jul 13, 2019 (153)
65 Qatari NC_000020.10 - 10300961 Apr 27, 2020 (154)
66 SGDP_PRJ NC_000020.10 - 10300961 Apr 27, 2020 (154)
67 Siberian NC_000020.10 - 10300961 Apr 27, 2020 (154)
68 8.3KJPN NC_000020.10 - 10300961 Apr 27, 2021 (155)
69 14KJPN NC_000020.11 - 10320313 Oct 13, 2022 (156)
70 TopMed NC_000020.11 - 10320313 Apr 27, 2021 (155)
71 UK 10K study - Twins NC_000020.10 - 10300961 Oct 12, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000020.10 - 10300961 Jul 13, 2019 (153)
73 ALFA NC_000020.11 - 10320313 Apr 27, 2021 (155)
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)
rs57112257 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85594364, ss113082917, ss169080429, ss283299831, ss1698594482 NC_000020.9:10248960:C:T NC_000020.11:10320312:C:T (self)
77502950, 42904192, 30322593, 5601832, 19116641, 46097932, 16533429, 20090908, 40748724, 10873821, 86808466, 42904192, 9471890, ss228256388, ss237762468, ss243949045, ss566135582, ss662006565, ss994538527, ss1082072960, ss1364063517, ss1579436893, ss1638411713, ss1681405746, ss1938048986, ss1969090798, ss2029803728, ss2158357467, ss2629398943, ss2704030738, ss2965429322, ss3017867341, ss3684584345, ss3743248564, ss3758421232, ss3835587776, ss3888731744, ss3938920538, ss5228839159, ss5436259275, ss5662864620, ss5845443900, ss5957766092 NC_000020.10:10300960:C:T NC_000020.11:10320312:C:T (self)
101691376, 546474553, 2070583, 38200429, 121664024, 357362605, 8885077398, ss2241324426, ss3028734861, ss3706558965, ss3821595026, ss3981822428, ss5082253660, ss5308084772, ss5500485384, ss5614165441, ss5787826920, ss5817815953, ss5853068764, ss5922673506 NC_000020.11:10320312:C:T NC_000020.11:10320312:C:T (self)
ss460007, ss4254927, ss8464938, ss24092329, ss156162149 NT_011387.8:10240960:C:T NC_000020.11:10320312: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 rs362554

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.post761+d5e8e07