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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.

rs115479960

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:18519 (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=0.066908 (17710/264690, TOPMED)
A=0.065703 (9008/137102, GnomAD)
A=0.06460 (1402/21702, ALFA) (+ 9 more)
A=0.0554 (355/6404, 1000G_30x)
A=0.0523 (262/5008, 1000G)
A=0.0586 (226/3854, ALSPAC)
A=0.0661 (245/3708, TWINSUK)
A=0.050 (50/998, GoNL)
A=0.022 (13/600, NorthernSweden)
A=0.019 (4/216, Qatari)
G=0.45 (19/42, SGDP_PRJ)
A=0.07 (3/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01986 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 21702 G=0.93540 A=0.06460
European Sub 14364 G=0.94751 A=0.05249
African Sub 5532 G=0.8995 A=0.1005
African Others Sub 196 G=0.847 A=0.153
African American Sub 5336 G=0.9014 A=0.0986
Asian Sub 146 G=1.000 A=0.000
East Asian Sub 120 G=1.000 A=0.000
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.959 A=0.041
Latin American 2 Sub 610 G=0.951 A=0.049
South Asian Sub 104 G=0.971 A=0.029
Other Sub 800 G=0.934 A=0.066


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=0.933092 A=0.066908
gnomAD - Genomes Global Study-wide 137102 G=0.934297 A=0.065703
gnomAD - Genomes European Sub 74838 G=0.94503 A=0.05497
gnomAD - Genomes African Sub 40512 G=0.90391 A=0.09609
gnomAD - Genomes American Sub 13280 G=0.94578 A=0.05422
gnomAD - Genomes Ashkenazi Jewish Sub 3308 G=0.9550 A=0.0450
gnomAD - Genomes East Asian Sub 3064 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2100 G=0.9376 A=0.0624
Allele Frequency Aggregator Total Global 21702 G=0.93540 A=0.06460
Allele Frequency Aggregator European Sub 14364 G=0.94751 A=0.05249
Allele Frequency Aggregator African Sub 5532 G=0.8995 A=0.1005
Allele Frequency Aggregator Other Sub 800 G=0.934 A=0.066
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.951 A=0.049
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.959 A=0.041
Allele Frequency Aggregator Asian Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=0.971 A=0.029
1000Genomes_30x Global Study-wide 6404 G=0.9446 A=0.0554
1000Genomes_30x African Sub 1786 G=0.8886 A=0.1114
1000Genomes_30x Europe Sub 1266 G=0.9471 A=0.0529
1000Genomes_30x South Asian Sub 1202 G=0.9692 A=0.0308
1000Genomes_30x East Asian Sub 1170 G=0.9983 A=0.0017
1000Genomes_30x American Sub 980 G=0.949 A=0.051
1000Genomes Global Study-wide 5008 G=0.9477 A=0.0523
1000Genomes African Sub 1322 G=0.8941 A=0.1059
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=0.9443 A=0.0557
1000Genomes South Asian Sub 978 G=0.968 A=0.032
1000Genomes American Sub 694 G=0.951 A=0.049
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9414 A=0.0586
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9339 A=0.0661
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.950 A=0.050
Northern Sweden ACPOP Study-wide 600 G=0.978 A=0.022
Qatari Global Study-wide 216 G=0.981 A=0.019
SGDP_PRJ Global Study-wide 42 G=0.45 A=0.55
The Danish reference pan genome Danish Study-wide 40 G=0.93 A=0.07
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 3 NC_000003.12:g.18519G>A
GRCh37.p13 chr 3 NC_000003.11:g.60197G>A
Gene: LINC01986, long intergenic non-protein coding RNA 1986 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01986 transcript NR_110824.1:n. 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 3 NC_000003.12:g.18519= NC_000003.12:g.18519G>A
GRCh37.p13 chr 3 NC_000003.11:g.60197= NC_000003.11:g.60197G>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#.

31 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss219921841 Jul 14, 2010 (132)
2 TISHKOFF ss556354861 Apr 25, 2013 (138)
3 EVA-GONL ss978164047 Aug 21, 2014 (142)
4 JMKIDD_LAB ss1070090306 Aug 21, 2014 (142)
5 1000GENOMES ss1302408209 Aug 21, 2014 (142)
6 EVA_GENOME_DK ss1579800265 Apr 01, 2015 (144)
7 EVA_DECODE ss1587622377 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1606204870 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1649198903 Apr 01, 2015 (144)
10 WEILL_CORNELL_DGM ss1921415458 Feb 12, 2016 (147)
11 ILLUMINA ss1958526841 Feb 12, 2016 (147)
12 JJLAB ss2021256215 Sep 14, 2016 (149)
13 GNOMAD ss2788465706 Nov 08, 2017 (151)
14 SWEGEN ss2991671591 Nov 08, 2017 (151)
15 ILLUMINA ss3022200957 Nov 08, 2017 (151)
16 CSHL ss3344833623 Nov 08, 2017 (151)
17 ILLUMINA ss3652666245 Oct 11, 2018 (152)
18 EVA_DECODE ss3708445524 Jul 13, 2019 (153)
19 ACPOP ss3729543904 Jul 13, 2019 (153)
20 EVA ss3759536282 Jul 13, 2019 (153)
21 KHV_HUMAN_GENOMES ss3802685186 Jul 13, 2019 (153)
22 SGDP_PRJ ss3855010917 Apr 25, 2020 (154)
23 TOPMED ss4551018205 Apr 26, 2021 (155)
24 1000G_HIGH_COVERAGE ss5252706743 Oct 13, 2022 (156)
25 EVA ss5337266997 Oct 13, 2022 (156)
26 EVA ss5506855291 Oct 13, 2022 (156)
27 1000G_HIGH_COVERAGE ss5530370892 Oct 13, 2022 (156)
28 SANFORD_IMAGENETICS ss5631338366 Oct 13, 2022 (156)
29 EVA ss5825209635 Oct 13, 2022 (156)
30 EVA ss5867239078 Oct 13, 2022 (156)
31 EVA ss5959593882 Oct 13, 2022 (156)
32 1000Genomes NC_000003.11 - 60197 Oct 11, 2018 (152)
33 1000Genomes_30x NC_000003.12 - 18519 Oct 13, 2022 (156)
34 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 60197 Oct 11, 2018 (152)
35 The Danish reference pan genome NC_000003.11 - 60197 Apr 25, 2020 (154)
36 gnomAD - Genomes NC_000003.12 - 18519 Apr 26, 2021 (155)
37 Genome of the Netherlands Release 5 NC_000003.11 - 60197 Apr 25, 2020 (154)
38 Northern Sweden NC_000003.11 - 60197 Jul 13, 2019 (153)
39 Qatari NC_000003.11 - 60197 Apr 25, 2020 (154)
40 SGDP_PRJ NC_000003.11 - 60197 Apr 25, 2020 (154)
41 TopMed NC_000003.12 - 18519 Apr 26, 2021 (155)
42 UK 10K study - Twins NC_000003.11 - 60197 Oct 11, 2018 (152)
43 ALFA NC_000003.12 - 18519 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
ss1587622377 NC_000003.10:35196:G:A NC_000003.12:18518:G:A (self)
13540558, 7503662, 5965204, 3289478, 2828769, 3457388, 7027897, 7503662, ss219921841, ss556354861, ss978164047, ss1070090306, ss1302408209, ss1579800265, ss1606204870, ss1649198903, ss1921415458, ss1958526841, ss2021256215, ss2788465706, ss2991671591, ss3022200957, ss3344833623, ss3652666245, ss3729543904, ss3759536282, ss3855010917, ss5337266997, ss5506855291, ss5631338366, ss5825209635, ss5959593882 NC_000003.11:60196:G:A NC_000003.12:18518:G:A (self)
17896827, 96340273, 388395760, 125022483, ss3708445524, ss3802685186, ss4551018205, ss5252706743, ss5530370892, ss5867239078 NC_000003.12:18518:G:A NC_000003.12:18518: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 rs115479960

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