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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.

rs4099234

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:28563 (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
A=0.07790 (924/11862, ALFA)
A=0.13274 (1466/11044, 8.3KJPN)
A=0.3163 (1214/3838, GnomAD) (+ 3 more)
A=0.1405 (363/2584, KOREAN)
A=0.018 (8/442, SGDP_PRJ)
A=0.06 (2/36, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIR1302-2 : 2KB Upstream Variant
MIR1302-2HG : 2KB Upstream Variant
WASH7P : Intron Variant
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.28563A>C
GRCh38.p13 chr 1 NC_000001.11:g.28563A>G
GRCh38.p13 chr 1 NC_000001.11:g.28563A>T
GRCh37.p13 chr 1 NC_000001.10:g.28563A>C
GRCh37.p13 chr 1 NC_000001.10:g.28563A>G
GRCh37.p13 chr 1 NC_000001.10:g.28563A>T
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1:n. N/A Intron Variant
Gene: MIR1302-2, microRNA 1302-2 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR1302-2 transcript NR_036051.1:n. N/A Upstream Transcript Variant
Gene: MIR1302-2HG, uncharacterized MIR1302-2HG (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR1302-2HG transcript variant X2 XR_001737835.1:n. N/A Upstream Transcript Variant
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 (New)
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 11862 A=0.07790 G=0.92210
European Sub 7618 A=0.0440 G=0.9560
African Sub 2816 A=0.1911 G=0.8089
African Others Sub 108 A=0.194 G=0.806
African American Sub 2708 A=0.1909 G=0.8091
Asian Sub 108 A=0.000 G=1.000
East Asian Sub 84 A=0.00 G=1.00
Other Asian Sub 24 A=0.00 G=1.00
Latin American 1 Sub 146 A=0.062 G=0.938
Latin American 2 Sub 610 A=0.018 G=0.982
South Asian Sub 94 A=0.02 G=0.98
Other Sub 470 A=0.062 G=0.938


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
Allele Frequency Aggregator Total Global 11862 A=0.07790 G=0.92210
Allele Frequency Aggregator European Sub 7618 A=0.0440 G=0.9560
Allele Frequency Aggregator African Sub 2816 A=0.1911 G=0.8089
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.018 G=0.982
Allele Frequency Aggregator Other Sub 470 A=0.062 G=0.938
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.062 G=0.938
Allele Frequency Aggregator Asian Sub 108 A=0.000 G=1.000
Allele Frequency Aggregator South Asian Sub 94 A=0.02 G=0.98
8.3KJPN JAPANESE Study-wide 11044 A=0.13274 G=0.86726
gnomAD - Genomes Global Study-wide 3838 A=0.3163 G=0.6837
gnomAD - Genomes African Sub 2332 A=0.4880 G=0.5120
gnomAD - Genomes European Sub 1050 A=0.0305 G=0.9695
gnomAD - Genomes American Sub 200 A=0.135 G=0.865
gnomAD - Genomes East Asian Sub 164 A=0.006 G=0.994
gnomAD - Genomes Other Sub 52 A=0.27 G=0.73
gnomAD - Genomes Ashkenazi Jewish Sub 40 A=0.05 G=0.95
KOREAN population from KRGDB KOREAN Study-wide 2584 A=0.1405 C=0.0000, G=0.8595, T=0.0000
SGDP_PRJ Global Study-wide 442 A=0.018 C=0.002, G=0.975, T=0.005
The Danish reference pan genome Danish Study-wide 36 A=0.06 G=0.94
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.28563= NC_000001.11:g.28563A>C NC_000001.11:g.28563A>G NC_000001.11:g.28563A>T
GRCh37.p13 chr 1 NC_000001.10:g.28563= NC_000001.10:g.28563A>C NC_000001.10:g.28563A>G NC_000001.10:g.28563A>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#.

19 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss5514976 Oct 10, 2002 (108)
2 SC_JCM ss5794108 Sep 28, 2016 (149)
3 BCMHGSC_JDW ss87152948 Mar 25, 2008 (129)
4 ENSEMBL ss139137690 Dec 01, 2009 (131)
5 BCM-HGSC-SUB ss205560186 Jul 04, 2010 (132)
6 GMI ss275679886 May 04, 2012 (142)
7 BILGI_BIOE ss538305550 Apr 25, 2013 (142)
8 SSMP ss647514788 Apr 25, 2013 (142)
9 DDI ss1425684532 Apr 01, 2015 (144)
10 EVA_GENOME_DK ss1573850687 Apr 01, 2015 (144)
11 GRF ss2697372934 Nov 08, 2017 (151)
12 GNOMAD ss2750602594 Nov 08, 2017 (151)
13 SWEGEN ss2986141652 Nov 08, 2017 (151)
14 TOPMED ss3066318412 Nov 08, 2017 (151)
15 CSHL ss3343271503 Nov 08, 2017 (151)
16 URBANLAB ss3646580283 Oct 11, 2018 (152)
17 SGDP_PRJ ss3847983549 Apr 25, 2020 (154)
18 KRGDB ss3892823311 Apr 25, 2020 (154)
19 TOMMO_GENOMICS ss5142031929 Apr 25, 2021 (155)
20 The Danish reference pan genome NC_000001.10 - 28563 Apr 25, 2020 (154)
21 gnomAD - Genomes NC_000001.11 - 28563 Apr 25, 2021 (155)
22 KOREAN population from KRGDB NC_000001.10 - 28563 Apr 25, 2020 (154)
23 SGDP_PRJ NC_000001.10 - 28563 Apr 25, 2020 (154)
24 8.3KJPN NC_000001.10 - 28563 Apr 25, 2021 (155)
25 ALFA NC_000001.11 - 28563 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).

Associated ID History Updated (Build)
rs200364216 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
705, 529, ss3847983549, ss3892823311 NC_000001.10:28562:A:C NC_000001.11:28562:A:C (self)
ss87152948, ss205560186, ss275679886 NC_000001.9:18425:A:G NC_000001.11:28562:A:G (self)
1357921, 705, 529, 1236, ss538305550, ss647514788, ss1425684532, ss1573850687, ss2697372934, ss2750602594, ss2986141652, ss3343271503, ss3847983549, ss3892823311, ss5142031929 NC_000001.10:28562:A:G NC_000001.11:28562:A:G (self)
2234, 91905054, ss3066318412, ss3646580283 NC_000001.11:28562:A:G NC_000001.11:28562:A:G (self)
ss5514976, ss5794108, ss139137690 NT_077402.2:18562:A:G NC_000001.11:28562:A:G (self)
705, 529, ss3847983549, ss3892823311 NC_000001.10:28562:A:T NC_000001.11:28562: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 rs4099234

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