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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.

rs9424286

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3799367 (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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.081650 (21612/264690, TOPMED)
T=0.066594 (9293/139548, GnomAD)
T=0.06060 (1138/18780, ALFA) (+ 13 more)
T=0.39895 (6684/16754, 8.3KJPN)
T=0.1963 (983/5008, 1000G)
T=0.0665 (298/4478, Estonian)
T=0.0532 (205/3854, ALSPAC)
T=0.0448 (166/3708, TWINSUK)
G=0.4956 (1450/2926, KOREAN)
G=0.4760 (872/1832, Korea1K)
T=0.045 (45/998, GoNL)
T=0.062 (37/600, NorthernSweden)
T=0.079 (17/216, Qatari)
G=0.346 (72/208, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
G=0.44 (14/32, 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 1 NC_000001.11:g.3799367G>A
GRCh38.p13 chr 1 NC_000001.11:g.3799367G>C
GRCh38.p13 chr 1 NC_000001.11:g.3799367G>T
GRCh37.p13 chr 1 NC_000001.10:g.3715931G>A
GRCh37.p13 chr 1 NC_000001.10:g.3715931G>C
GRCh37.p13 chr 1 NC_000001.10:g.3715931G>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 18780 G=0.93940 A=0.00000, T=0.06060
European Sub 14204 G=0.94628 A=0.00000, T=0.05372
African Sub 2918 G=0.9681 A=0.0000, T=0.0319
African Others Sub 114 G=1.000 A=0.000, T=0.000
African American Sub 2804 G=0.9668 A=0.0000, T=0.0332
Asian Sub 112 G=0.589 A=0.000, T=0.411
East Asian Sub 86 G=0.58 A=0.00, T=0.42
Other Asian Sub 26 G=0.62 A=0.00, T=0.38
Latin American 1 Sub 146 G=0.911 A=0.000, T=0.089
Latin American 2 Sub 610 G=0.797 A=0.000, T=0.203
South Asian Sub 98 G=0.64 A=0.00, T=0.36
Other Sub 692 G=0.908 A=0.000, T=0.092


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=0.918350 T=0.081650
gnomAD - Genomes Global Study-wide 139548 G=0.933406 T=0.066594
gnomAD - Genomes European Sub 75668 G=0.94431 T=0.05569
gnomAD - Genomes African Sub 41762 G=0.96384 T=0.03616
gnomAD - Genomes American Sub 13554 G=0.87812 T=0.12188
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.9638 T=0.0362
gnomAD - Genomes East Asian Sub 3108 G=0.4801 T=0.5199
gnomAD - Genomes Other Sub 2138 G=0.9153 T=0.0847
8.3KJPN JAPANESE Study-wide 16754 G=0.60105 T=0.39895
1000Genomes Global Study-wide 5008 G=0.8037 T=0.1963
1000Genomes African Sub 1322 G=0.9720 T=0.0280
1000Genomes East Asian Sub 1008 G=0.4812 T=0.5188
1000Genomes Europe Sub 1006 G=0.9453 T=0.0547
1000Genomes South Asian Sub 978 G=0.711 T=0.289
1000Genomes American Sub 694 G=0.878 T=0.122
Genetic variation in the Estonian population Estonian Study-wide 4478 G=0.9335 T=0.0665
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9468 T=0.0532
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9552 T=0.0448
KOREAN population from KRGDB KOREAN Study-wide 2926 G=0.4956 C=0.0000, T=0.5044
Korean Genome Project KOREAN Study-wide 1832 G=0.4760 T=0.5240
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.955 T=0.045
Northern Sweden ACPOP Study-wide 600 G=0.938 T=0.062
Qatari Global Study-wide 216 G=0.921 T=0.079
SGDP_PRJ Global Study-wide 208 G=0.346 T=0.654
The Danish reference pan genome Danish Study-wide 40 G=0.88 T=0.12
Siberian Global Study-wide 32 G=0.44 T=0.56
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 C T
GRCh38.p13 chr 1 NC_000001.11:g.3799367= NC_000001.11:g.3799367G>A NC_000001.11:g.3799367G>C NC_000001.11:g.3799367G>T
GRCh37.p13 chr 1 NC_000001.10:g.3715931= NC_000001.10:g.3715931G>A NC_000001.10:g.3715931G>C NC_000001.10:g.3715931G>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#.

36 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992566 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss16396608 Feb 27, 2004 (120)
3 ABI ss41092513 Mar 13, 2006 (126)
4 GMI ss275691398 May 04, 2012 (137)
5 GMI ss283990987 Apr 25, 2013 (138)
6 1000GENOMES ss328376455 May 09, 2011 (134)
7 TISHKOFF ss553734594 Apr 25, 2013 (138)
8 SSMP ss647536353 Apr 25, 2013 (138)
9 EVA-GONL ss974796307 Aug 21, 2014 (142)
10 JMKIDD_LAB ss1067627201 Aug 21, 2014 (142)
11 1000GENOMES ss1289451196 Aug 21, 2014 (142)
12 EVA_GENOME_DK ss1573860072 Apr 01, 2015 (144)
13 EVA_DECODE ss1584155092 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1599427112 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1642421145 Apr 01, 2015 (144)
16 WEILL_CORNELL_DGM ss1917991843 Feb 12, 2016 (147)
17 JJLAB ss2019512042 Sep 14, 2016 (149)
18 USC_VALOUEV ss2147502438 Dec 20, 2016 (150)
19 HUMAN_LONGEVITY ss2159573725 Dec 20, 2016 (150)
20 TOPMED ss2321728632 Dec 20, 2016 (150)
21 SYSTEMSBIOZJU ss2624271780 Nov 08, 2017 (151)
22 GRF ss2697396455 Nov 08, 2017 (151)
23 GNOMAD ss2750971045 Nov 08, 2017 (151)
24 SWEGEN ss2986201115 Nov 08, 2017 (151)
25 TOPMED ss3067123798 Nov 08, 2017 (151)
26 CSHL ss3343288866 Nov 08, 2017 (151)
27 EGCUT_WGS ss3654302322 Jul 12, 2019 (153)
28 EVA_DECODE ss3686046966 Jul 12, 2019 (153)
29 ACPOP ss3726739905 Jul 12, 2019 (153)
30 EVA ss3745755139 Jul 12, 2019 (153)
31 KHV_HUMAN_GENOMES ss3798776858 Jul 12, 2019 (153)
32 SGDP_PRJ ss3848069285 Apr 25, 2020 (154)
33 KRGDB ss3892930795 Apr 25, 2020 (154)
34 KOGIC ss3943692631 Apr 25, 2020 (154)
35 TOPMED ss4437301858 Apr 25, 2021 (155)
36 TOMMO_GENOMICS ss5142201208 Apr 25, 2021 (155)
37 1000Genomes NC_000001.10 - 3715931 Oct 11, 2018 (152)
38 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3715931 Oct 11, 2018 (152)
39 Genetic variation in the Estonian population NC_000001.10 - 3715931 Oct 11, 2018 (152)
40 The Danish reference pan genome NC_000001.10 - 3715931 Apr 25, 2020 (154)
41 gnomAD - Genomes NC_000001.11 - 3799367 Apr 25, 2021 (155)
42 Genome of the Netherlands Release 5 NC_000001.10 - 3715931 Apr 25, 2020 (154)
43 KOREAN population from KRGDB NC_000001.10 - 3715931 Apr 25, 2020 (154)
44 Korean Genome Project NC_000001.11 - 3799367 Apr 25, 2020 (154)
45 Northern Sweden NC_000001.10 - 3715931 Jul 12, 2019 (153)
46 Qatari NC_000001.10 - 3715931 Apr 25, 2020 (154)
47 SGDP_PRJ NC_000001.10 - 3715931 Apr 25, 2020 (154)
48 Siberian NC_000001.10 - 3715931 Apr 25, 2020 (154)
49 8.3KJPN NC_000001.10 - 3715931 Apr 25, 2021 (155)
50 TopMed NC_000001.11 - 3799367 Apr 25, 2021 (155)
51 UK 10K study - Twins NC_000001.10 - 3715931 Oct 11, 2018 (152)
52 ALFA NC_000001.11 - 3799367 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
3227950361 NC_000001.11:3799366:G:A NC_000001.11:3799366:G:A
108189, ss3892930795 NC_000001.10:3715930:G:C NC_000001.11:3799366:G:C (self)
ss275691398, ss283990987, ss1584155092 NC_000001.9:3705790:G:T NC_000001.11:3799366:G:T (self)
119212, 53332, 40570, 1367306, 22921, 108189, 24770, 33773, 86265, 18792, 170515, 53332, ss328376455, ss553734594, ss647536353, ss974796307, ss1067627201, ss1289451196, ss1573860072, ss1599427112, ss1642421145, ss1917991843, ss2019512042, ss2147502438, ss2321728632, ss2624271780, ss2697396455, ss2750971045, ss2986201115, ss3343288866, ss3654302322, ss3726739905, ss3745755139, ss3848069285, ss3892930795, ss5142201208 NC_000001.10:3715930:G:T NC_000001.11:3799366:G:T (self)
860604, 70632, 565318, 908193, 3227950361, ss2159573725, ss3067123798, ss3686046966, ss3798776858, ss3943692631, ss4437301858 NC_000001.11:3799366:G:T NC_000001.11:3799366:G:T (self)
ss12992566, ss16396608 NT_004321.15:1022704:G:T NC_000001.11:3799366:G:T (self)
ss41092513 NT_004350.19:3194562:G:T NC_000001.11:3799366:G: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 rs9424286

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