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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.

rs2541696

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:38165 (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
C>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.032506 (8604/264690, TOPMED)
A=0.030995 (4346/140218, GnomAD)
A=0.006632 (838/126362, ALFA) (+ 11 more)
A=0.0344 (220/6404, 1000G_30x)
A=0.0321 (161/5008, 1000G)
A=0.0005 (2/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.001 (1/998, GoNL)
A=0.087 (87/996, HapMap)
A=0.006 (3/534, MGP)
A=0.009 (2/214, Qatari)
A=0.00 (0/90, Ancient Sardinia)
C=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, 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 126362 C=0.993368 A=0.006632
European Sub 110566 C=0.999114 A=0.000886
African Sub 6634 C=0.9014 A=0.0986
African Others Sub 238 C=0.857 A=0.143
African American Sub 6396 C=0.9031 A=0.0969
Asian Sub 622 C=1.000 A=0.000
East Asian Sub 490 C=1.000 A=0.000
Other Asian Sub 132 C=1.000 A=0.000
Latin American 1 Sub 678 C=0.979 A=0.021
Latin American 2 Sub 2210 C=0.9946 A=0.0054
South Asian Sub 184 C=1.000 A=0.000
Other Sub 5468 C=0.9890 A=0.0110


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 C=0.967494 A=0.032506
gnomAD - Genomes Global Study-wide 140218 C=0.969005 A=0.030995
gnomAD - Genomes European Sub 75942 C=0.99957 A=0.00043
gnomAD - Genomes African Sub 42016 C=0.90149 A=0.09851
gnomAD - Genomes American Sub 13658 C=0.99063 A=0.00937
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 C=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2150 C=0.9791 A=0.0209
Allele Frequency Aggregator Total Global 126362 C=0.993368 A=0.006632
Allele Frequency Aggregator European Sub 110566 C=0.999114 A=0.000886
Allele Frequency Aggregator African Sub 6634 C=0.9014 A=0.0986
Allele Frequency Aggregator Other Sub 5468 C=0.9890 A=0.0110
Allele Frequency Aggregator Latin American 2 Sub 2210 C=0.9946 A=0.0054
Allele Frequency Aggregator Latin American 1 Sub 678 C=0.979 A=0.021
Allele Frequency Aggregator Asian Sub 622 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 184 C=1.000 A=0.000
1000Genomes_30x Global Study-wide 6404 C=0.9656 A=0.0344
1000Genomes_30x African Sub 1786 C=0.8813 A=0.1187
1000Genomes_30x Europe Sub 1266 C=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 A=0.0000
1000Genomes_30x American Sub 980 C=0.992 A=0.008
1000Genomes Global Study-wide 5008 C=0.9679 A=0.0321
1000Genomes African Sub 1322 C=0.8828 A=0.1172
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=1.0000 A=0.0000
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=0.991 A=0.009
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9995 A=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 A=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.999 A=0.001
HapMap Global Study-wide 996 C=0.913 A=0.087
HapMap African Sub 692 C=0.886 A=0.114
HapMap American Sub 216 C=0.963 A=0.037
HapMap Asian Sub 88 C=1.00 A=0.00
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.994 A=0.006
Qatari Global Study-wide 214 C=0.991 A=0.009
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 90 C=1.00 A=0.00
SGDP_PRJ Global Study-wide 8 C=0.5 A=0.5
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 16 NC_000016.10:g.38165C>A
GRCh37.p13 chr 16 NC_000016.9:g.88165C>A
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 C= A
GRCh38.p14 chr 16 NC_000016.10:g.38165= NC_000016.10:g.38165C>A
GRCh37.p13 chr 16 NC_000016.9:g.88165= NC_000016.9:g.88165C>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#.

56 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3563062 Sep 28, 2001 (100)
2 ILLUMINA ss75119631 Dec 06, 2007 (129)
3 ILLUMINA-UK ss118150365 Feb 14, 2009 (130)
4 KRIBB_YJKIM ss119438638 Dec 01, 2009 (131)
5 ILLUMINA ss160557520 Dec 01, 2009 (131)
6 ILLUMINA ss173385615 Jul 04, 2010 (132)
7 1000GENOMES ss227085788 Jul 14, 2010 (132)
8 ILLUMINA ss480599294 May 04, 2012 (137)
9 ILLUMINA ss480613524 May 04, 2012 (137)
10 ILLUMINA ss481444267 Sep 08, 2015 (146)
11 ILLUMINA ss485094792 May 04, 2012 (137)
12 ILLUMINA ss537102194 Sep 08, 2015 (146)
13 TISHKOFF ss564710009 Apr 25, 2013 (138)
14 ILLUMINA ss778499424 Sep 08, 2015 (146)
15 ILLUMINA ss782993700 Sep 08, 2015 (146)
16 ILLUMINA ss783954405 Sep 08, 2015 (146)
17 ILLUMINA ss832250564 Sep 08, 2015 (146)
18 ILLUMINA ss833955514 Sep 08, 2015 (146)
19 EVA-GONL ss992173230 Aug 21, 2014 (142)
20 1000GENOMES ss1354950846 Aug 21, 2014 (142)
21 DDI ss1427745402 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1633790742 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1676784775 Apr 01, 2015 (144)
24 EVA_MGP ss1711412584 Apr 01, 2015 (144)
25 ILLUMINA ss1752211889 Sep 08, 2015 (146)
26 HAMMER_LAB ss1808371027 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1935578275 Feb 12, 2016 (147)
28 ILLUMINA ss2633280749 Nov 08, 2017 (151)
29 GNOMAD ss2939122938 Nov 08, 2017 (151)
30 ILLUMINA ss3627453155 Oct 12, 2018 (152)
31 ILLUMINA ss3631270346 Oct 12, 2018 (152)
32 ILLUMINA ss3633110879 Oct 12, 2018 (152)
33 ILLUMINA ss3633816139 Oct 12, 2018 (152)
34 ILLUMINA ss3634625837 Oct 12, 2018 (152)
35 ILLUMINA ss3635504719 Oct 12, 2018 (152)
36 ILLUMINA ss3636316666 Oct 12, 2018 (152)
37 ILLUMINA ss3637256084 Oct 12, 2018 (152)
38 ILLUMINA ss3638107736 Oct 12, 2018 (152)
39 ILLUMINA ss3640333157 Oct 12, 2018 (152)
40 ILLUMINA ss3643090239 Oct 12, 2018 (152)
41 EVA_DECODE ss3698629103 Jul 13, 2019 (153)
42 ILLUMINA ss3744926331 Jul 13, 2019 (153)
43 ILLUMINA ss3772424808 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3818854462 Jul 13, 2019 (153)
45 SGDP_PRJ ss3883708495 Apr 27, 2020 (154)
46 EVA ss3985740356 Apr 26, 2021 (155)
47 EVA ss4017721675 Apr 26, 2021 (155)
48 TOPMED ss5004236266 Apr 26, 2021 (155)
49 1000G_HIGH_COVERAGE ss5299753435 Oct 16, 2022 (156)
50 EVA ss5421630530 Oct 16, 2022 (156)
51 HUGCELL_USP ss5493330881 Oct 16, 2022 (156)
52 1000G_HIGH_COVERAGE ss5601805003 Oct 16, 2022 (156)
53 SANFORD_IMAGENETICS ss5658253122 Oct 16, 2022 (156)
54 EVA ss5845956167 Oct 16, 2022 (156)
55 EVA ss5897860725 Oct 16, 2022 (156)
56 EVA ss5949680373 Oct 16, 2022 (156)
57 1000Genomes NC_000016.9 - 88165 Oct 12, 2018 (152)
58 1000Genomes_30x NC_000016.10 - 38165 Oct 16, 2022 (156)
59 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 88165 Oct 12, 2018 (152)
60 gnomAD - Genomes NC_000016.10 - 38165 Apr 26, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000016.9 - 88165 Apr 27, 2020 (154)
62 HapMap NC_000016.10 - 38165 Apr 27, 2020 (154)
63 Medical Genome Project healthy controls from Spanish population NC_000016.9 - 88165 Apr 27, 2020 (154)
64 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000016.9 - 88165 Apr 26, 2021 (155)
65 Qatari NC_000016.9 - 88165 Apr 27, 2020 (154)
66 SGDP_PRJ NC_000016.9 - 88165 Apr 27, 2020 (154)
67 TopMed NC_000016.10 - 38165 Apr 26, 2021 (155)
68 UK 10K study - Twins NC_000016.9 - 88165 Oct 12, 2018 (152)
69 ALFA NC_000016.10 - 38165 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss118150365, ss480599294, ss3643090239 NC_000016.8:28164:C:A NC_000016.10:38164:C:A (self)
68075431, 37808061, 16869838, 528344, 966283, 17620197, 35725475, 37808061, ss227085788, ss480613524, ss481444267, ss485094792, ss537102194, ss564710009, ss778499424, ss782993700, ss783954405, ss832250564, ss833955514, ss992173230, ss1354950846, ss1427745402, ss1633790742, ss1676784775, ss1711412584, ss1752211889, ss1808371027, ss1935578275, ss2633280749, ss2939122938, ss3627453155, ss3631270346, ss3633110879, ss3633816139, ss3634625837, ss3635504719, ss3636316666, ss3637256084, ss3638107736, ss3640333157, ss3744926331, ss3772424808, ss3883708495, ss3985740356, ss4017721675, ss5421630530, ss5658253122, ss5845956167, ss5949680373 NC_000016.9:88164:C:A NC_000016.10:38164:C:A (self)
89330938, 479812908, 1332238, 219781927, 3144656003, ss3698629103, ss3818854462, ss5004236266, ss5299753435, ss5493330881, ss5601805003, ss5897860725 NC_000016.10:38164:C:A NC_000016.10:38164:C:A (self)
ss3563062, ss75119631, ss119438638, ss160557520, ss173385615 NT_010393.16:28164:C:A NC_000016.10:38164:C: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 rs2541696

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