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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.

rs708748

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:226563822 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.066602 (17629/264690, TOPMED)
A=0.063169 (8858/140226, GnomAD)
A=0.03137 (1302/41510, ALFA) (+ 9 more)
A=0.0595 (381/6404, 1000G_30x)
A=0.0567 (284/5008, 1000G)
A=0.0003 (1/3854, ALSPAC)
A=0.0003 (1/3708, TWINSUK)
A=0.0978 (135/1380, HapMap)
A=0.0026 (3/1136, Daghestan)
A=0.010 (6/626, Chileans)
A=0.019 (4/216, Qatari)
G=0.47 (15/32, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
STUM : Intron Variant
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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 41510 G=0.96863 A=0.03137 0.942375 0.005107 0.052517 32
European Sub 25878 G=0.99857 A=0.00143 0.99714 0.0 0.00286 0
African Sub 5612 G=0.8027 A=0.1973 0.641839 0.036351 0.32181 0
African Others Sub 192 G=0.724 A=0.276 0.489583 0.041667 0.46875 2
African American Sub 5420 G=0.8055 A=0.1945 0.647232 0.036162 0.316605 0
Asian Sub 486 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 388 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 638 G=0.947 A=0.053 0.893417 0.0 0.106583 1
Latin American 2 Sub 5046 G=0.9869 A=0.0131 0.974237 0.000396 0.025367 0
South Asian Sub 174 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 3676 G=0.9842 A=0.0158 0.970076 0.001632 0.028292 8


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=0.933398 A=0.066602
gnomAD - Genomes Global Study-wide 140226 G=0.936831 A=0.063169
gnomAD - Genomes European Sub 75952 G=0.99839 A=0.00161
gnomAD - Genomes African Sub 42002 G=0.80299 A=0.19701
gnomAD - Genomes American Sub 13668 G=0.97717 A=0.02283
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9952 A=0.0048
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9381 A=0.0619
Allele Frequency Aggregator Total Global 41510 G=0.96863 A=0.03137
Allele Frequency Aggregator European Sub 25878 G=0.99857 A=0.00143
Allele Frequency Aggregator African Sub 5612 G=0.8027 A=0.1973
Allele Frequency Aggregator Latin American 2 Sub 5046 G=0.9869 A=0.0131
Allele Frequency Aggregator Other Sub 3676 G=0.9842 A=0.0158
Allele Frequency Aggregator Latin American 1 Sub 638 G=0.947 A=0.053
Allele Frequency Aggregator Asian Sub 486 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 174 G=1.000 A=0.000
1000Genomes_30x Global Study-wide 6404 G=0.9405 A=0.0595
1000Genomes_30x African Sub 1786 G=0.8018 A=0.1982
1000Genomes_30x Europe Sub 1266 G=0.9953 A=0.0047
1000Genomes_30x South Asian Sub 1202 G=0.9983 A=0.0017
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.981 A=0.019
1000Genomes Global Study-wide 5008 G=0.9433 A=0.0567
1000Genomes African Sub 1322 G=0.7988 A=0.2012
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9970 A=0.0030
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=0.980 A=0.020
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 A=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 A=0.0003
HapMap Global Study-wide 1380 G=0.9022 A=0.0978
HapMap African Sub 692 G=0.838 A=0.162
HapMap American Sub 422 G=0.948 A=0.052
HapMap Europe Sub 176 G=0.994 A=0.006
HapMap Asian Sub 90 G=1.00 A=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1136 G=0.9974 A=0.0026
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=1.000 A=0.000
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.979 A=0.021
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=1.000 A=0.000
Genome-wide autozygosity in Daghestan Europe Sub 108 G=1.000 A=0.000
Genome-wide autozygosity in Daghestan South Asian Sub 98 G=1.00 A=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=1.00 A=0.00
Chileans Chilean Study-wide 626 G=0.990 A=0.010
Qatari Global Study-wide 216 G=0.981 A=0.019
SGDP_PRJ Global Study-wide 32 G=0.47 A=0.53
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 1 NC_000001.11:g.226563822G>A
GRCh37.p13 chr 1 NC_000001.10:g.226751523G>A
Gene: STUM, stum, mechanosensory transduction mediator homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
STUM transcript variant 1 NM_001003665.4:c.202+1471…

NM_001003665.4:c.202+14716G>A

 		N/A Intron Variant
STUM transcript variant X1 XM_011544183.4:c.202+1471…

XM_011544183.4:c.202+14716G>A

 		N/A Intron 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
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
GRCh38.p14 chr 1 NC_000001.11:g.226563822= NC_000001.11:g.226563822G>A
GRCh37.p13 chr 1 NC_000001.10:g.226751523= NC_000001.10:g.226751523G>A
STUM transcript NM_001003665.3:c.202+14716= NM_001003665.3:c.202+14716G>A
STUM transcript variant 1 NM_001003665.4:c.202+14716= NM_001003665.4:c.202+14716G>A
STUM transcript variant X1 XM_011544183.4:c.202+14716= XM_011544183.4:c.202+14716G>A
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#.

41 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1167792 Oct 04, 2000 (86)
2 KWOK ss1170215 Oct 04, 2000 (86)
3 TSC-CSHL ss1443480 Oct 05, 2000 (92)
4 KWOK ss2030656 Oct 18, 2000 (87)
5 KWOK ss2031106 Oct 18, 2000 (87)
6 KWOK ss2031731 Oct 18, 2000 (87)
7 KWOK ss2032698 Oct 18, 2000 (87)
8 SC_JCM ss2624525 Nov 08, 2000 (89)
9 PERLEGEN ss23187204 Sep 20, 2004 (123)
10 ABI ss44025855 Mar 14, 2006 (126)
11 AFFY ss76599850 Dec 08, 2007 (130)
12 KRIBB_YJKIM ss104824634 Feb 06, 2009 (130)
13 1000GENOMES ss111870848 Jan 25, 2009 (130)
14 ILLUMINA ss160845108 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss165304883 Jul 04, 2010 (132)
16 1000GENOMES ss218916743 Jul 14, 2010 (132)
17 ILLUMINA ss482464794 Sep 08, 2015 (146)
18 TISHKOFF ss555179730 Apr 25, 2013 (138)
19 JMKIDD_LAB ss1068654922 Aug 21, 2014 (142)
20 1000GENOMES ss1294916826 Aug 21, 2014 (142)
21 HAMMER_LAB ss1397274410 Sep 08, 2015 (146)
22 EVA_UK10K_ALSPAC ss1602282174 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1645276207 Apr 01, 2015 (144)
24 HAMMER_LAB ss1795820026 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1919437014 Feb 12, 2016 (147)
26 HUMAN_LONGEVITY ss2170639391 Dec 20, 2016 (150)
27 GNOMAD ss2766978848 Nov 08, 2017 (151)
28 SWEGEN ss2988561388 Nov 08, 2017 (151)
29 ILLUMINA ss3636055128 Oct 11, 2018 (152)
30 EVA_DECODE ss3688760894 Jul 12, 2019 (153)
31 KHV_HUMAN_GENOMES ss3800421780 Jul 12, 2019 (153)
32 SGDP_PRJ ss3851037063 Apr 25, 2020 (154)
33 TOPMED ss4485939290 Apr 25, 2021 (155)
34 1000G_HIGH_COVERAGE ss5246029878 Oct 12, 2022 (156)
35 EVA ss5325217145 Oct 12, 2022 (156)
36 HUGCELL_USP ss5446441754 Oct 12, 2022 (156)
37 1000G_HIGH_COVERAGE ss5520246063 Oct 12, 2022 (156)
38 SANFORD_IMAGENETICS ss5627579476 Oct 12, 2022 (156)
39 EVA ss5833356726 Oct 12, 2022 (156)
40 EVA ss5912241276 Oct 12, 2022 (156)
41 EVA ss5939423781 Oct 12, 2022 (156)
42 1000Genomes NC_000001.10 - 226751523 Oct 11, 2018 (152)
43 1000Genomes_30x NC_000001.11 - 226563822 Oct 12, 2022 (156)
44 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 226751523 Oct 11, 2018 (152)
45 Chileans NC_000001.10 - 226751523 Apr 25, 2020 (154)
46 Genome-wide autozygosity in Daghestan NC_000001.9 - 224818146 Apr 25, 2020 (154)
47 gnomAD - Genomes NC_000001.11 - 226563822 Apr 25, 2021 (155)
48 HapMap NC_000001.11 - 226563822 Apr 25, 2020 (154)
49 Qatari NC_000001.10 - 226751523 Apr 25, 2020 (154)
50 SGDP_PRJ NC_000001.10 - 226751523 Apr 25, 2020 (154)
51 TopMed NC_000001.11 - 226563822 Apr 25, 2021 (155)
52 UK 10K study - Twins NC_000001.10 - 226751523 Oct 11, 2018 (152)
53 ALFA NC_000001.11 - 226563822 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)
rs987905 Jan 18, 2001 (92)
rs56524975 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
35515, ss111870848, ss165304883, ss1397274410 NC_000001.9:224818145:G:A NC_000001.11:226563821:G:A (self)
5781069, 3195315, 34788, 1478944, 3054043, 3195315, ss218916743, ss482464794, ss555179730, ss1068654922, ss1294916826, ss1602282174, ss1645276207, ss1795820026, ss1919437014, ss2766978848, ss2988561388, ss3636055128, ss3851037063, ss5325217145, ss5627579476, ss5833356726, ss5939423781 NC_000001.10:226751522:G:A NC_000001.11:226563821:G:A (self)
7771998, 41520443, 282453, 49545625, 5063040707, ss2170639391, ss3688760894, ss3800421780, ss4485939290, ss5246029878, ss5446441754, ss5520246063, ss5912241276 NC_000001.11:226563821:G:A NC_000001.11:226563821:G:A (self)
ss1167792, ss1170215, ss1443480, ss2030656, ss2031106, ss2031731, ss2032698, ss2624525, ss23187204, ss44025855, ss76599850, ss104824634, ss160845108 NT_167186.1:20269301:G:A NC_000001.11:226563821:G:A (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 rs708748

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.post820+afb47a3d