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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.

rs9419555

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:90196 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.048978 (12964/264690, TOPMED)
A=0.047221 (6606/139894, GnomAD)
A=0.00658 (165/25072, ALFA) (+ 6 more)
A=0.0483 (242/5008, 1000G)
A=0.0005 (2/3854, ALSPAC)
A=0.0005 (2/3708, TWINSUK)
A=0.028 (6/216, Qatari)
A=0.000 (0/204, HapMap)
G=0.46 (11/24, 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 10 NC_000010.11:g.90196G>A
GRCh38.p13 chr 10 NC_000010.11:g.90196G>T
GRCh37.p13 chr 10 NC_000010.10:g.136136G>A
GRCh37.p13 chr 10 NC_000010.10:g.136136G>T
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.80196G>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.80196G>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 25072 G=0.99342 A=0.00658, T=0.00000
European Sub 20244 G=0.99921 A=0.00079, T=0.00000
African Sub 2588 G=0.9505 A=0.0495, T=0.0000
African Others Sub 102 G=0.931 A=0.069, T=0.000
African American Sub 2486 G=0.9513 A=0.0487, T=0.0000
Asian Sub 128 G=1.000 A=0.000, T=0.000
East Asian Sub 100 G=1.00 A=0.00, T=0.00
Other Asian Sub 28 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 160 G=0.975 A=0.025, T=0.000
Latin American 2 Sub 684 G=0.999 A=0.001, T=0.000
South Asian Sub 114 G=1.000 A=0.000, T=0.000
Other Sub 1154 G=0.9861 A=0.0139, T=0.0000


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=0.951022 A=0.048978
gnomAD - Genomes Global Study-wide 139894 G=0.952779 A=0.047221
gnomAD - Genomes European Sub 75802 G=0.99904 A=0.00096
gnomAD - Genomes African Sub 41884 G=0.85185 A=0.14815
gnomAD - Genomes American Sub 13624 G=0.98407 A=0.01593
gnomAD - Genomes Ashkenazi Jewish Sub 3308 G=0.9933 A=0.0067
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2146 G=0.9585 A=0.0415
1000Genomes Global Study-wide 5008 G=0.9517 A=0.0483
1000Genomes African Sub 1322 G=0.8260 A=0.1740
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.983 A=0.017
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9995 A=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9995 A=0.0005
Qatari Global Study-wide 216 G=0.972 A=0.028
HapMap Global Study-wide 204 G=1.000 A=0.000
HapMap American Sub 120 G=1.000 A=0.000
HapMap Asian Sub 84 G=1.00 A=0.00
SGDP_PRJ Global Study-wide 24 G=0.46 A=0.54
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 T
GRCh38.p13 chr 10 NC_000010.11:g.90196= NC_000010.11:g.90196G>A NC_000010.11:g.90196G>T
GRCh37.p13 chr 10 NC_000010.10:g.136136= NC_000010.10:g.136136G>A NC_000010.10:g.136136G>T
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.80196= NW_003571043.1:g.80196G>A NW_003571043.1:g.80196G>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#.

32 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12973483 Dec 05, 2003 (119)
2 HGSV ss80959086 Dec 16, 2007 (130)
3 1000GENOMES ss115221613 Jan 25, 2009 (130)
4 ILLUMINA-UK ss118963273 Feb 15, 2009 (130)
5 COMPLETE_GENOMICS ss168823588 Jul 04, 2010 (132)
6 1000GENOMES ss224512398 Jul 14, 2010 (132)
7 ILLUMINA ss482415474 May 04, 2012 (137)
8 ILLUMINA ss482502207 May 04, 2012 (137)
9 ILLUMINA ss534639433 Sep 11, 2015 (146)
10 TISHKOFF ss561707945 Apr 25, 2013 (138)
11 ILLUMINA ss780002456 Sep 11, 2015 (146)
12 ILLUMINA ss781753903 Sep 11, 2015 (146)
13 ILLUMINA ss835482155 Sep 11, 2015 (146)
14 JMKIDD_LAB ss1076687429 Aug 21, 2014 (142)
15 1000GENOMES ss1335913000 Aug 21, 2014 (142)
16 EVA_DECODE ss1596744283 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1623797635 Apr 09, 2015 (144)
18 EVA_UK10K_TWINSUK ss1666791668 Apr 09, 2015 (144)
19 WEILL_CORNELL_DGM ss1930414785 Feb 17, 2016 (147)
20 HUMAN_LONGEVITY ss2171932874 Dec 20, 2016 (150)
21 TOPMED ss2334635491 Oct 12, 2018 (152)
22 ILLUMINA ss2632661396 Oct 12, 2018 (152)
23 GNOMAD ss2884519442 Oct 12, 2018 (152)
24 SWEGEN ss3005784460 Oct 12, 2018 (152)
25 TOPMED ss3109332890 Nov 08, 2017 (151)
26 ILLUMINA ss3626364344 Oct 12, 2018 (152)
27 ILLUMINA ss3630689708 Oct 12, 2018 (152)
28 ILLUMINA ss3641655092 Oct 12, 2018 (152)
29 KHV_HUMAN_GENOMES ss3812993367 Jul 13, 2019 (153)
30 SGDP_PRJ ss3873326498 Apr 26, 2020 (154)
31 GNOMAD ss4211411335 Apr 26, 2021 (155)
32 TOPMED ss4839524573 Apr 26, 2021 (155)
33 1000Genomes NC_000010.10 - 136136 Oct 12, 2018 (152)
34 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 136136 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000010.11 - 90196 Apr 26, 2021 (155)
36 HapMap NC_000010.11 - 90196 Apr 26, 2020 (154)
37 Qatari NC_000010.10 - 136136 Apr 26, 2020 (154)
38 SGDP_PRJ NC_000010.10 - 136136 Apr 26, 2020 (154)
39 TopMed NC_000010.11 - 90196 Apr 26, 2021 (155)
40 UK 10K study - Twins NC_000010.10 - 136136 Oct 12, 2018 (152)
41 ALFA NC_000010.11 - 90196 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).

Associated ID History Updated (Build)
rs61559791 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss80959086 NC_000010.8:126135:G:A NC_000010.11:90195:G:A (self)
ss115221613, ss118963273, ss168823588, ss482502207, ss1596744283 NC_000010.9:126135:G:A NC_000010.11:90195:G:A (self)
48246710, 26806423, 12456715, 25343478, 26806423, ss224512398, ss482415474, ss534639433, ss561707945, ss780002456, ss781753903, ss835482155, ss1076687429, ss1335913000, ss1623797635, ss1666791668, ss1930414785, ss2334635491, ss2632661396, ss2884519442, ss3005784460, ss3626364344, ss3630689708, ss3641655092, ss3873326498 NC_000010.10:136135:G:A NC_000010.11:90195:G:A (self)
340934522, 317113, 34602928, 55070228, 10458338102, ss2171932874, ss3109332890, ss3812993367, ss4211411335, ss4839524573 NC_000010.11:90195:G:A NC_000010.11:90195:G:A (self)
ss12973483 NT_024115.14:76135:G:A NC_000010.11:90195:G:A (self)
10458338102 NC_000010.11:90195:G:T NC_000010.11:90195:G:T
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 rs9419555

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