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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.

rs117662806

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:40914 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.119525 (31637/264690, TOPMED)
A=0.118780 (16553/139358, GnomAD)
A=0.13049 (2465/18890, ALFA) (+ 10 more)
A=0.0773 (387/5008, 1000G)
A=0.1127 (505/4480, Estonian)
A=0.1448 (558/3854, ALSPAC)
A=0.1561 (579/3708, TWINSUK)
A=0.167 (100/600, NorthernSweden)
A=0.238 (51/214, Qatari)
G=0.44 (44/100, SGDP_PRJ)
A=0.17 (7/40, GENOME_DK)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
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.p13 chr 16 NC_000016.10:g.40914G>A
GRCh37.p13 chr 16 NC_000016.9:g.90914G>A
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

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 18890 G=0.86951 A=0.13049
European Sub 14286 G=0.85230 A=0.14770
African Sub 2946 G=0.9430 A=0.0570
African Others Sub 114 G=0.939 A=0.061
African American Sub 2832 G=0.9431 A=0.0569
Asian Sub 112 G=0.991 A=0.009
East Asian Sub 86 G=0.99 A=0.01
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.808 A=0.192
Latin American 2 Sub 610 G=0.880 A=0.120
South Asian Sub 98 G=0.95 A=0.05
Other Sub 692 G=0.884 A=0.116


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 G=0.880475 A=0.119525
gnomAD - Genomes Global Study-wide 139358 G=0.881220 A=0.118780
gnomAD - Genomes European Sub 75480 G=0.85268 A=0.14732
gnomAD - Genomes African Sub 41754 G=0.93833 A=0.06167
gnomAD - Genomes American Sub 13556 G=0.86987 A=0.13013
gnomAD - Genomes Ashkenazi Jewish Sub 3314 G=0.7610 A=0.2390
gnomAD - Genomes East Asian Sub 3116 G=0.9990 A=0.0010
gnomAD - Genomes Other Sub 2138 G=0.8601 A=0.1399
1000Genomes Global Study-wide 5008 G=0.9227 A=0.0773
1000Genomes African Sub 1322 G=0.9501 A=0.0499
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.8390 A=0.1610
1000Genomes South Asian Sub 978 G=0.928 A=0.072
1000Genomes American Sub 694 G=0.872 A=0.128
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8873 A=0.1127
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8552 A=0.1448
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8439 A=0.1561
Northern Sweden ACPOP Study-wide 600 G=0.833 A=0.167
Qatari Global Study-wide 214 G=0.762 A=0.238
SGDP_PRJ Global Study-wide 100 G=0.44 A=0.56
The Danish reference pan genome Danish Study-wide 40 G=0.82 A=0.17
Siberian Global Study-wide 4 G=0.5 A=0.5
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 G= A
GRCh38.p13 chr 16 NC_000016.10:g.40914= NC_000016.10:g.40914G>A
GRCh37.p13 chr 16 NC_000016.9:g.90914= NC_000016.9:g.90914G>A
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#.

30 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss236913579 Jul 15, 2010 (132)
2 SSMP ss660454712 Apr 25, 2013 (138)
3 EVA-GONL ss992173268 Aug 21, 2014 (142)
4 JMKIDD_LAB ss1080408295 Aug 21, 2014 (142)
5 1000GENOMES ss1354950959 Aug 21, 2014 (142)
6 DDI ss1427745423 Apr 01, 2015 (144)
7 EVA_GENOME_DK ss1577790924 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1633790798 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1676784831 Apr 01, 2015 (144)
10 EVA_DECODE ss1696205823 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1935578312 Feb 12, 2016 (147)
12 JJLAB ss2028576445 Sep 14, 2016 (149)
13 USC_VALOUEV ss2156983775 Nov 08, 2017 (151)
14 HUMAN_LONGEVITY ss2209766282 Dec 20, 2016 (150)
15 TOPMED ss2374358996 Dec 20, 2016 (150)
16 GNOMAD ss2939123210 Nov 08, 2017 (151)
17 SWEGEN ss3013892132 Nov 08, 2017 (151)
18 BIOINF_KMB_FNS_UNIBA ss3028112979 Nov 08, 2017 (151)
19 TOPMED ss3237331808 Nov 08, 2017 (151)
20 CSHL ss3351285360 Nov 08, 2017 (151)
21 EGCUT_WGS ss3681020625 Jul 13, 2019 (153)
22 EVA_DECODE ss3698629161 Jul 13, 2019 (153)
23 ACPOP ss3741245914 Jul 13, 2019 (153)
24 PACBIO ss3787952294 Jul 13, 2019 (153)
25 PACBIO ss3792948367 Jul 13, 2019 (153)
26 PACBIO ss3797833108 Jul 13, 2019 (153)
27 KHV_HUMAN_GENOMES ss3818854507 Jul 13, 2019 (153)
28 EVA ss3834421841 Apr 27, 2020 (154)
29 SGDP_PRJ ss3883708559 Apr 27, 2020 (154)
30 TOPMED ss5004237047 Apr 26, 2021 (155)
31 1000Genomes NC_000016.9 - 90914 Oct 12, 2018 (152)
32 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 90914 Oct 12, 2018 (152)
33 Genetic variation in the Estonian population NC_000016.9 - 90914 Oct 12, 2018 (152)
34 The Danish reference pan genome NC_000016.9 - 90914 Apr 27, 2020 (154)
35 gnomAD - Genomes NC_000016.10 - 40914 Apr 26, 2021 (155)
36 Northern Sweden NC_000016.9 - 90914 Jul 13, 2019 (153)
37 Qatari NC_000016.9 - 90914 Apr 27, 2020 (154)
38 SGDP_PRJ NC_000016.9 - 90914 Apr 27, 2020 (154)
39 Siberian NC_000016.9 - 90914 Apr 27, 2020 (154)
40 TopMed NC_000016.10 - 40914 Apr 26, 2021 (155)
41 UK 10K study - Twins NC_000016.9 - 90914 Oct 12, 2018 (152)
42 ALFA NC_000016.10 - 40914 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1696205823 NC_000016.8:30913:G:A NC_000016.10:40913:G:A (self)
68075547, 37808122, 26758873, 4008339, 14530779, 17620234, 35725539, 9500129, 37808122, ss236913579, ss660454712, ss992173268, ss1080408295, ss1354950959, ss1427745423, ss1577790924, ss1633790798, ss1676784831, ss1935578312, ss2028576445, ss2156983775, ss2374358996, ss2939123210, ss3013892132, ss3351285360, ss3681020625, ss3741245914, ss3787952294, ss3792948367, ss3797833108, ss3834421841, ss3883708559 NC_000016.9:90913:G:A NC_000016.10:40913:G:A (self)
479813562, 137412674, 219782708, 15247608180, ss2209766282, ss3028112979, ss3237331808, ss3698629161, ss3818854507, ss5004237047 NC_000016.10:40913:G:A NC_000016.10:40913:G:A (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 rs117662806

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