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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.

rs6699990

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:821532 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.024134 (6388/264690, TOPMED)
G=0.029525 (3570/120916, GnomAD)
G=0.01398 (248/17740, ALFA) (+ 10 more)
C=0.00125 (21/16760, 8.3KJPN)
G=0.0086 (43/5008, 1000G)
G=0.0374 (144/3854, ALSPAC)
G=0.0375 (139/3708, TWINSUK)
C=0.0024 (7/2922, KOREAN)
G=0.048 (48/998, GoNL)
G=0.030 (18/600, NorthernSweden)
G=0.028 (6/216, Qatari)
A=0.50 (6/12, SGDP_PRJ)
G=0.50 (6/12, SGDP_PRJ)
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 1 NC_000001.11:g.821532A>C
GRCh38.p13 chr 1 NC_000001.11:g.821532A>G
GRCh38.p13 chr 1 NC_000001.11:g.821532A>T
GRCh37.p13 chr 1 NC_000001.10:g.756912A>C
GRCh37.p13 chr 1 NC_000001.10:g.756912A>G
GRCh37.p13 chr 1 NC_000001.10:g.756912A>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

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 17740 A=0.98602 C=0.00000, G=0.01398, T=0.00000
European Sub 13494 A=0.98177 C=0.00000, G=0.01823, T=0.00000
African Sub 2838 A=1.0000 C=0.0000, G=0.0000, T=0.0000
African Others Sub 114 A=1.000 C=0.000, G=0.000, T=0.000
African American Sub 2724 A=1.0000 C=0.0000, G=0.0000, T=0.0000
Asian Sub 112 A=1.000 C=0.000, G=0.000, T=0.000
East Asian Sub 86 A=1.00 C=0.00, G=0.00, T=0.00
Other Asian Sub 26 A=1.00 C=0.00, G=0.00, T=0.00
Latin American 1 Sub 140 A=1.000 C=0.000, G=0.000, T=0.000
Latin American 2 Sub 582 A=1.000 C=0.000, G=0.000, T=0.000
South Asian Sub 94 A=1.00 C=0.00, G=0.00, T=0.00
Other Sub 480 A=0.996 C=0.000, G=0.004, T=0.000


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 A=0.975866 G=0.024134
gnomAD - Genomes Global Study-wide 120916 A=0.970475 G=0.029525
gnomAD - Genomes European Sub 66448 A=0.95821 G=0.04179
gnomAD - Genomes African Sub 35028 A=0.99132 G=0.00868
gnomAD - Genomes American Sub 12056 A=0.97304 G=0.02696
gnomAD - Genomes East Asian Sub 2804 A=1.0000 G=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2770 A=0.9581 G=0.0419
gnomAD - Genomes Other Sub 1810 A=0.9735 G=0.0265
8.3KJPN JAPANESE Study-wide 16760 A=0.99875 C=0.00125
1000Genomes Global Study-wide 5008 A=0.9914 G=0.0086
1000Genomes African Sub 1322 A=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9761 G=0.0239
1000Genomes South Asian Sub 978 A=0.991 G=0.009
1000Genomes American Sub 694 A=0.986 G=0.014
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9626 G=0.0374
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9625 G=0.0375
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9976 C=0.0024
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.952 G=0.048
Northern Sweden ACPOP Study-wide 600 A=0.970 G=0.030
Qatari Global Study-wide 216 A=0.972 G=0.028
SGDP_PRJ Global Study-wide 12 A=0.50 G=0.50
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 A= C G T
GRCh38.p13 chr 1 NC_000001.11:g.821532= NC_000001.11:g.821532A>C NC_000001.11:g.821532A>G NC_000001.11:g.821532A>T
GRCh37.p13 chr 1 NC_000001.10:g.756912= NC_000001.10:g.756912A>C NC_000001.10:g.756912A>G NC_000001.10:g.756912A>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#.

25 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9897446 Jul 11, 2003 (116)
2 1000GENOMES ss107938270 Jan 22, 2009 (130)
3 1000GENOMES ss328357467 May 09, 2011 (134)
4 EVA-GONL ss974769263 Aug 21, 2014 (142)
5 1000GENOMES ss1289338928 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1599378303 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1642372336 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1917960212 Feb 12, 2016 (147)
9 JJLAB ss2019498385 Sep 14, 2016 (149)
10 HUMAN_LONGEVITY ss2159368091 Dec 20, 2016 (150)
11 TOPMED ss2321502809 Dec 20, 2016 (150)
12 GNOMAD ss2750637151 Nov 08, 2017 (151)
13 SWEGEN ss2986148739 Nov 08, 2017 (151)
14 TOPMED ss3066396753 Nov 08, 2017 (151)
15 TOPMED ss3066396754 Nov 08, 2017 (151)
16 TOPMED ss3066396755 Nov 08, 2017 (151)
17 EVA_DECODE ss3685991995 Jul 12, 2019 (153)
18 EVA_DECODE ss3685991996 Jul 12, 2019 (153)
19 ACPOP ss3726716277 Jul 12, 2019 (153)
20 EVA ss3745720870 Jul 12, 2019 (153)
21 EVA ss3825981435 Apr 25, 2020 (154)
22 SGDP_PRJ ss3847995014 Apr 25, 2020 (154)
23 KRGDB ss3892835365 Apr 25, 2020 (154)
24 TOPMED ss4436429867 Apr 25, 2021 (155)
25 TOMMO_GENOMICS ss5142051365 Apr 25, 2021 (155)
26 1000Genomes NC_000001.10 - 756912 Oct 11, 2018 (152)
27 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 756912 Oct 11, 2018 (152)
28 gnomAD - Genomes NC_000001.11 - 821532 Apr 25, 2021 (155)
29 Genome of the Netherlands Release 5 NC_000001.10 - 756912 Apr 25, 2020 (154)
30 KOREAN population from KRGDB NC_000001.10 - 756912 Apr 25, 2020 (154)
31 Northern Sweden NC_000001.10 - 756912 Jul 12, 2019 (153)
32 Qatari NC_000001.10 - 756912 Apr 25, 2020 (154)
33 SGDP_PRJ NC_000001.10 - 756912 Apr 25, 2020 (154)
34 8.3KJPN NC_000001.10 - 756912 Apr 25, 2021 (155)
35 TopMed NC_000001.11 - 821532 Apr 25, 2021 (155)
36 UK 10K study - Twins NC_000001.10 - 756912 Oct 11, 2018 (152)
37 ALFA NC_000001.11 - 821532 Apr 25, 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
12759, 20672, ss3892835365, ss5142051365 NC_000001.10:756911:A:C NC_000001.11:821531:A:C (self)
9178508621, ss3066396753, ss3685991995 NC_000001.11:821531:A:C NC_000001.11:821531:A:C (self)
ss107938270 NC_000001.9:746774:A:G NC_000001.11:821531:A:G (self)
3642, 193, 336, 1142, 2142, 11994, 193, ss328357467, ss974769263, ss1289338928, ss1599378303, ss1642372336, ss1917960212, ss2019498385, ss2321502809, ss2750637151, ss2986148739, ss3726716277, ss3745720870, ss3825981435, ss3847995014 NC_000001.10:756911:A:G NC_000001.11:821531:A:G (self)
62043, 15055, 36202, 9178508621, ss2159368091, ss3066396754, ss3685991996, ss4436429867 NC_000001.11:821531:A:G NC_000001.11:821531:A:G (self)
ss9897446 NT_034471.3:235543:A:G NC_000001.11:821531:A:G (self)
9178508621, ss3066396755 NC_000001.11:821531:A:T NC_000001.11:821531:A: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 rs6699990

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