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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.

rs244406

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:110800585 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.016295 (4313/264690, TOPMED)
T=0.01606 (1277/79528, GnomAD)
T=0.06592 (1862/28248, 14KJPN) (+ 9 more)
T=0.06837 (1124/16440, 8.3KJPN)
T=0.00947 (133/14050, ALFA)
T=0.0331 (212/6404, 1000G_30x)
T=0.0339 (170/5008, 1000G)
T=0.0650 (190/2922, KOREAN)
T=0.0686 (123/1794, Korea1K)
T=0.004 (2/518, NorthernSweden)
T=0.014 (3/216, Qatari)
G=0.45 (17/38, SGDP_PRJ)
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 14050 G=0.99053 T=0.00947
European Sub 9690 G=0.9966 T=0.0034
African Sub 2898 G=0.9976 T=0.0024
African Others Sub 114 G=1.000 T=0.000
African American Sub 2784 G=0.9975 T=0.0025
Asian Sub 112 G=0.920 T=0.080
East Asian Sub 86 G=0.92 T=0.08
Other Asian Sub 26 G=0.92 T=0.08
Latin American 1 Sub 146 G=0.979 T=0.021
Latin American 2 Sub 610 G=0.903 T=0.097
South Asian Sub 98 G=0.95 T=0.05
Other Sub 496 G=0.966 T=0.034


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=0.983705 T=0.016295
gnomAD - Genomes Global Study-wide 79528 G=0.98394 T=0.01606
gnomAD - Genomes African Sub 37382 G=0.99783 T=0.00217
gnomAD - Genomes European Sub 27856 G=0.99347 T=0.00653
gnomAD - Genomes American Sub 8554 G=0.9092 T=0.0908
gnomAD - Genomes East Asian Sub 2328 G=0.9158 T=0.0842
gnomAD - Genomes Ashkenazi Jewish Sub 2056 G=0.9946 T=0.0054
gnomAD - Genomes Other Sub 1352 G=0.9778 T=0.0222
14KJPN JAPANESE Study-wide 28248 G=0.93408 T=0.06592
8.3KJPN JAPANESE Study-wide 16440 G=0.93163 T=0.06837
Allele Frequency Aggregator Total Global 14050 G=0.99053 T=0.00947
Allele Frequency Aggregator European Sub 9690 G=0.9966 T=0.0034
Allele Frequency Aggregator African Sub 2898 G=0.9976 T=0.0024
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.903 T=0.097
Allele Frequency Aggregator Other Sub 496 G=0.966 T=0.034
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.979 T=0.021
Allele Frequency Aggregator Asian Sub 112 G=0.920 T=0.080
Allele Frequency Aggregator South Asian Sub 98 G=0.95 T=0.05
1000Genomes_30x Global Study-wide 6404 G=0.9669 T=0.0331
1000Genomes_30x African Sub 1786 G=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9984 T=0.0016
1000Genomes_30x South Asian Sub 1202 G=0.9484 T=0.0516
1000Genomes_30x East Asian Sub 1170 G=0.9282 T=0.0718
1000Genomes_30x American Sub 980 G=0.935 T=0.065
1000Genomes Global Study-wide 5008 G=0.9661 T=0.0339
1000Genomes African Sub 1322 G=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 G=0.9276 T=0.0724
1000Genomes Europe Sub 1006 G=0.9920 T=0.0080
1000Genomes South Asian Sub 978 G=0.956 T=0.044
1000Genomes American Sub 694 G=0.937 T=0.063
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9350 T=0.0650
Korean Genome Project KOREAN Study-wide 1794 G=0.9314 T=0.0686
Northern Sweden ACPOP Study-wide 518 G=0.996 T=0.004
Qatari Global Study-wide 216 G=0.986 T=0.014
SGDP_PRJ Global Study-wide 38 G=0.45 T=0.55
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 5 NC_000005.10:g.110800585G>T
GRCh37.p13 chr 5 NC_000005.9:g.110136285G>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= T
GRCh38.p14 chr 5 NC_000005.10:g.110800585= NC_000005.10:g.110800585G>T
GRCh37.p13 chr 5 NC_000005.9:g.110136285= NC_000005.9:g.110136285G>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, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss314160 Jul 12, 2000 (79)
2 KWOK ss314831 Jul 12, 2000 (85)
3 SC_JCM ss638726 Jul 16, 2000 (80)
4 KWOK ss1116104 Oct 04, 2000 (86)
5 KWOK ss1117161 Oct 04, 2000 (86)
6 KWOK ss2033892 Oct 18, 2000 (87)
7 KWOK ss2034303 Oct 18, 2000 (87)
8 KWOK ss2034802 Oct 18, 2000 (96)
9 GMI ss278425726 May 04, 2012 (137)
10 1000GENOMES ss1316582700 Aug 21, 2014 (142)
11 WEILL_CORNELL_DGM ss1925209776 Feb 12, 2016 (147)
12 JJLAB ss2023211462 Sep 14, 2016 (149)
13 HUMAN_LONGEVITY ss2276820309 Dec 20, 2016 (150)
14 GRF ss2706925622 Nov 08, 2017 (151)
15 GNOMAD ss2828972443 Nov 08, 2017 (151)
16 SWEGEN ss2997540527 Nov 08, 2017 (151)
17 EVA_DECODE ss3715399520 Jul 13, 2019 (153)
18 ACPOP ss3732680245 Jul 13, 2019 (153)
19 KHV_HUMAN_GENOMES ss3807042927 Jul 13, 2019 (153)
20 SGDP_PRJ ss3862647246 Apr 26, 2020 (154)
21 KRGDB ss3909259913 Apr 26, 2020 (154)
22 KOGIC ss3957367412 Apr 26, 2020 (154)
23 TOPMED ss4673182888 Apr 26, 2021 (155)
24 TOMMO_GENOMICS ss5173444627 Apr 26, 2021 (155)
25 EVA ss5359958077 Oct 17, 2022 (156)
26 HUGCELL_USP ss5463317323 Oct 17, 2022 (156)
27 1000G_HIGH_COVERAGE ss5549649250 Oct 17, 2022 (156)
28 SANFORD_IMAGENETICS ss5638562763 Oct 17, 2022 (156)
29 TOMMO_GENOMICS ss5710324510 Oct 17, 2022 (156)
30 YY_MCH ss5806635791 Oct 17, 2022 (156)
31 EVA ss5835429533 Oct 17, 2022 (156)
32 EVA ss5895681442 Oct 17, 2022 (156)
33 1000Genomes NC_000005.9 - 110136285 Oct 12, 2018 (152)
34 1000Genomes_30x NC_000005.10 - 110800585 Oct 17, 2022 (156)
35 gnomAD - Genomes NC_000005.10 - 110800585 Apr 26, 2021 (155)
36 KOREAN population from KRGDB NC_000005.9 - 110136285 Apr 26, 2020 (154)
37 Korean Genome Project NC_000005.10 - 110800585 Apr 26, 2020 (154)
38 Northern Sweden NC_000005.9 - 110136285 Jul 13, 2019 (153)
39 Qatari NC_000005.9 - 110136285 Apr 26, 2020 (154)
40 SGDP_PRJ NC_000005.9 - 110136285 Apr 26, 2020 (154)
41 8.3KJPN NC_000005.9 - 110136285 Apr 26, 2021 (155)
42 14KJPN NC_000005.10 - 110800585 Oct 17, 2022 (156)
43 TopMed NC_000005.10 - 110800585 Apr 26, 2021 (155)
44 ALFA NC_000005.10 - 110800585 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)
rs244921 Sep 19, 2000 (85)
rs1288889 Oct 23, 2000 (87)
rs1289133 Jun 15, 2001 (96)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss278425726 NC_000005.8:110164183:G:T NC_000005.10:110800584:G:T (self)
28239437, 16437307, 5965110, 7251706, 14664226, 31413934, ss1316582700, ss1925209776, ss2023211462, ss2706925622, ss2828972443, ss2997540527, ss3732680245, ss3862647246, ss3909259913, ss5173444627, ss5359958077, ss5638562763, ss5835429533 NC_000005.9:110136284:G:T NC_000005.10:110800584:G:T (self)
37175185, 199779601, 13745413, 44161614, 510560445, 1386302524, ss2276820309, ss3715399520, ss3807042927, ss3957367412, ss4673182888, ss5463317323, ss5549649250, ss5710324510, ss5806635791, ss5895681442 NC_000005.10:110800584:G:T NC_000005.10:110800584:G:T (self)
ss314160, ss314831, ss638726, ss1116104, ss1117161, ss2033892, ss2034303, ss2034802 NT_034772.6:18450156:G:T NC_000005.10:110800584: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 rs244406

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