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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs4458297

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:16765102 (GRCh38.p14) 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=0.429570 (113703/264690, TOPMED)
A=0.431928 (59968/138838, GnomAD)
A=0.24843 (7020/28258, 14KJPN) (+ 6 more)
A=0.00057 (9/15682, 8.3KJPN)
A=0.4060 (2600/6404, 1000G_30x)
A=0.1656 (959/5790, ALFA)
A=0.2715 (795/2928, KOREAN)
A=0.2904 (532/1832, Korea1K)
G=0.38 (10/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 5790 G=0.8344 A=0.1656, T=0.0000
European Sub 4384 G=0.7945 A=0.2055, T=0.0000
African Sub 766 G=0.949 A=0.051, T=0.000
African Others Sub 30 G=0.93 A=0.07, T=0.00
African American Sub 736 G=0.950 A=0.050, T=0.000
Asian Sub 54 G=0.98 A=0.02, T=0.00
East Asian Sub 40 G=1.00 A=0.00, T=0.00
Other Asian Sub 14 G=0.93 A=0.07, T=0.00
Latin American 1 Sub 54 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 314 G=1.000 A=0.000, T=0.000
South Asian Sub 40 G=1.00 A=0.00, T=0.00
Other Sub 178 G=0.899 A=0.101, 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 G=0.570430 A=0.429570
gnomAD - Genomes Global Study-wide 138838 G=0.568072 A=0.431928
gnomAD - Genomes European Sub 75276 G=0.59542 A=0.40458
gnomAD - Genomes African Sub 41712 G=0.49012 A=0.50988
gnomAD - Genomes American Sub 13382 G=0.64250 A=0.35750
gnomAD - Genomes Ashkenazi Jewish Sub 3302 G=0.4952 A=0.5048
gnomAD - Genomes East Asian Sub 3054 G=0.6938 A=0.3062
gnomAD - Genomes Other Sub 2112 G=0.5933 A=0.4067
14KJPN JAPANESE Study-wide 28258 G=0.75157 A=0.24843
8.3KJPN JAPANESE Study-wide 15682 G=0.99943 A=0.00057
1000Genomes_30x Global Study-wide 6404 G=0.5940 A=0.4060
1000Genomes_30x African Sub 1786 G=0.4563 A=0.5437
1000Genomes_30x Europe Sub 1266 G=0.5727 A=0.4273
1000Genomes_30x South Asian Sub 1202 G=0.5940 A=0.4060
1000Genomes_30x East Asian Sub 1170 G=0.7222 A=0.2778
1000Genomes_30x American Sub 980 G=0.719 A=0.281
Allele Frequency Aggregator Total Global 5790 G=0.8344 A=0.1656, T=0.0000
Allele Frequency Aggregator European Sub 4384 G=0.7945 A=0.2055, T=0.0000
Allele Frequency Aggregator African Sub 766 G=0.949 A=0.051, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 314 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Other Sub 178 G=0.899 A=0.101, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 54 G=1.00 A=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 54 G=0.98 A=0.02, T=0.00
Allele Frequency Aggregator South Asian Sub 40 G=1.00 A=0.00, T=0.00
KOREAN population from KRGDB KOREAN Study-wide 2928 G=0.7285 A=0.2715
Korean Genome Project KOREAN Study-wide 1832 G=0.7096 A=0.2904
Siberian Global Study-wide 26 G=0.38 A=0.62
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.p14 chr 22 NC_000022.11:g.16765102G>A
GRCh38.p14 chr 22 NC_000022.11:g.16765102G>T
GRCh37.p13 chr 22 NC_000022.10:g.17245992G>A
GRCh37.p13 chr 22 NC_000022.10:g.17245992G>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
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.p14 chr 22 NC_000022.11:g.16765102= NC_000022.11:g.16765102G>A NC_000022.11:g.16765102G>T
GRCh37.p13 chr 22 NC_000022.10:g.17245992= NC_000022.10:g.17245992G>A NC_000022.10:g.17245992G>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#.

33 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5984968 Feb 20, 2003 (111)
2 WI_SSAHASNP ss12526759 Jul 11, 2003 (116)
3 SC_SNP ss13347462 Dec 05, 2003 (119)
4 SSAHASNP ss21837471 Apr 05, 2004 (121)
5 ABI ss41543029 Mar 13, 2006 (126)
6 BCMHGSC_JDW ss91868795 Mar 24, 2008 (129)
7 ENSEMBL ss138331622 Dec 01, 2009 (131)
8 ENSEMBL ss139837816 Dec 01, 2009 (131)
9 BL ss255829786 May 09, 2011 (142)
10 GMI ss283576873 May 04, 2012 (142)
11 PJP ss292732091 May 09, 2011 (142)
12 SSMP ss662466920 Apr 25, 2013 (142)
13 USC_VALOUEV ss2158761355 Dec 20, 2016 (150)
14 GRF ss2704500137 Nov 08, 2017 (151)
15 URBANLAB ss3651146556 Oct 12, 2018 (152)
16 EVA_DECODE ss3707912071 Jul 13, 2019 (153)
17 PACBIO ss3788786657 Jul 13, 2019 (153)
18 PACBIO ss3793658516 Jul 13, 2019 (153)
19 PACBIO ss3798544811 Jul 13, 2019 (153)
20 KHV_HUMAN_GENOMES ss3822371630 Jul 13, 2019 (153)
21 EVA ss3841586754 Apr 27, 2020 (154)
22 EVA ss3847101473 Apr 27, 2020 (154)
23 KRGDB ss3940576441 Apr 27, 2020 (154)
24 KOGIC ss3983338834 Apr 27, 2020 (154)
25 GNOMAD ss4362202254 Apr 27, 2021 (155)
26 TOPMED ss5104444518 Apr 27, 2021 (155)
27 TOMMO_GENOMICS ss5231933268 Apr 27, 2021 (155)
28 1000G_HIGH_COVERAGE ss5310582952 Oct 16, 2022 (156)
29 EVA ss5440396317 Oct 16, 2022 (156)
30 1000G_HIGH_COVERAGE ss5617906542 Oct 16, 2022 (156)
31 TOMMO_GENOMICS ss5792843673 Oct 16, 2022 (156)
32 YY_MCH ss5818573749 Oct 16, 2022 (156)
33 EVA ss5881272761 Oct 16, 2022 (156)
34 1000Genomes_30x NC_000022.11 - 16765102 Oct 16, 2022 (156)
35 gnomAD - Genomes NC_000022.11 - 16765102 Apr 27, 2021 (155)
36 KOREAN population from KRGDB NC_000022.10 - 17245992 Apr 27, 2020 (154)
37 Korean Genome Project NC_000022.11 - 16765102 Apr 27, 2020 (154)
38 Siberian NC_000022.10 - 17245992 Apr 27, 2020 (154)
39 8.3KJPN NC_000022.10 - 17245992 Apr 27, 2021 (155)
40 14KJPN NC_000022.11 - 16765102 Oct 16, 2022 (156)
41 TopMed NC_000022.11 - 16765102 Apr 27, 2021 (155)
42 ALFA NC_000022.11 - 16765102 Apr 27, 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)
rs138721688 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91868795, ss255829786, ss283576873, ss292732091 NC_000022.9:15625991:G:A NC_000022.11:16765101:G:A (self)
47753835, 11277709, 89902575, ss662466920, ss2158761355, ss2704500137, ss3788786657, ss3793658516, ss3798544811, ss3841586754, ss3940576441, ss5231933268, ss5440396317 NC_000022.10:17245991:G:A NC_000022.11:16765101:G:A (self)
105432477, 565949848, 39716835, 126680777, 379553465, 11599486095, ss3651146556, ss3707912071, ss3822371630, ss3847101473, ss3983338834, ss4362202254, ss5104444518, ss5310582952, ss5617906542, ss5792843673, ss5818573749, ss5881272761 NC_000022.11:16765101:G:A NC_000022.11:16765101:G:A (self)
ss5984968, ss12526759, ss13347462, ss21837471, ss41543029, ss138331622, ss139837816 NT_011519.10:398141:G:A NC_000022.11:16765101:G:A (self)
11599486095 NC_000022.11:16765101:G:T NC_000022.11:16765101: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 rs4458297

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.post761+d5e8e07