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dbSNP Short Genetic Variations

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.

rs323951

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83131384 (GRCh38.p13) 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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.069111 (18293/264690, TOPMED)
G=0.066795 (9354/140040, GnomAD)
G=0.03078 (875/28424, ALFA) (+ 7 more)
G=0.0673 (337/5008, 1000G)
G=0.0003 (1/3854, ALSPAC)
G=0.0003 (1/3708, TWINSUK)
G=0.1367 (163/1192, HapMap)
G=0.064 (40/626, Chileans)
G=0.028 (6/216, Qatari)
A=0.40 (8/20, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01362 : Intron Variant
LOC107985037 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.83131384A>G
GRCh37.p13 chr 1 NC_000001.10:g.83597067A>G
Gene: LINC01362, long intergenic non-protein coding RNA 1362 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01362 transcript NR_147074.1:n. N/A Intron Variant
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1: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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 28424 A=0.96922 G=0.03078
European Sub 21622 A=0.99912 G=0.00088
African Sub 3810 A=0.7945 G=0.2055
African Others Sub 134 A=0.709 G=0.291
African American Sub 3676 A=0.7976 G=0.2024
Asian Sub 174 A=1.000 G=0.000
East Asian Sub 114 A=1.000 G=0.000
Other Asian Sub 60 A=1.00 G=0.00
Latin American 1 Sub 228 A=0.939 G=0.061
Latin American 2 Sub 838 A=0.988 G=0.012
South Asian Sub 126 A=1.000 G=0.000
Other Sub 1626 A=0.9699 G=0.0301


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 A=0.930889 G=0.069111
gnomAD - Genomes Global Study-wide 140040 A=0.933205 G=0.066795
gnomAD - Genomes European Sub 75874 A=0.99938 G=0.00062
gnomAD - Genomes African Sub 41934 A=0.78655 G=0.21345
gnomAD - Genomes American Sub 13634 A=0.98225 G=0.01775
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3130 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 A=0.9470 G=0.0530
Allele Frequency Aggregator Total Global 28424 A=0.96922 G=0.03078
Allele Frequency Aggregator European Sub 21622 A=0.99912 G=0.00088
Allele Frequency Aggregator African Sub 3810 A=0.7945 G=0.2055
Allele Frequency Aggregator Other Sub 1626 A=0.9699 G=0.0301
Allele Frequency Aggregator Latin American 2 Sub 838 A=0.988 G=0.012
Allele Frequency Aggregator Latin American 1 Sub 228 A=0.939 G=0.061
Allele Frequency Aggregator Asian Sub 174 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 126 A=1.000 G=0.000
1000Genomes Global Study-wide 5008 A=0.9327 G=0.0673
1000Genomes African Sub 1322 A=0.7579 G=0.2421
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.976 G=0.024
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9997 G=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9997 G=0.0003
HapMap Global Study-wide 1192 A=0.8633 G=0.1367
HapMap African Sub 688 A=0.810 G=0.190
HapMap American Sub 414 A=0.923 G=0.077
HapMap Asian Sub 90 A=1.00 G=0.00
Chileans Chilean Study-wide 626 A=0.936 G=0.064
Qatari Global Study-wide 216 A=0.972 G=0.028
SGDP_PRJ Global Study-wide 20 A=0.40 G=0.60
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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.83131384= NC_000001.11:g.83131384A>G
GRCh37.p13 chr 1 NC_000001.10:g.83597067= NC_000001.10:g.83597067A>G
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, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss414356 Jul 12, 2000 (79)
2 SC_JCM ss595365 Jul 16, 2000 (80)
3 KWOK ss1023555 Oct 04, 2000 (86)
4 SC_SNP ss13020154 Dec 05, 2003 (119)
5 PERLEGEN ss23145055 Sep 20, 2004 (123)
6 ABI ss44072045 Mar 14, 2006 (126)
7 AFFY ss76843494 Dec 06, 2007 (129)
8 HGSV ss85945310 Dec 15, 2007 (130)
9 HGSV ss86165783 Dec 15, 2007 (130)
10 KRIBB_YJKIM ss104815087 Feb 06, 2009 (130)
11 ILLUMINA-UK ss118850806 Feb 14, 2009 (130)
12 1000GENOMES ss210573150 Jul 14, 2010 (132)
13 1000GENOMES ss218492057 Jul 14, 2010 (132)
14 ILLUMINA ss480776508 May 04, 2012 (137)
15 ILLUMINA ss482416648 May 04, 2012 (137)
16 ILLUMINA ss533938728 Sep 08, 2015 (146)
17 TISHKOFF ss554362551 Apr 25, 2013 (138)
18 ILLUMINA ss779790337 Aug 21, 2014 (142)
19 ILLUMINA ss781315417 Aug 21, 2014 (142)
20 ILLUMINA ss835266183 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1068043932 Aug 21, 2014 (142)
22 1000GENOMES ss1291670591 Aug 21, 2014 (142)
23 EVA_DECODE ss1584740011 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1600583805 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1643577838 Apr 01, 2015 (144)
26 EVA_SVP ss1712348380 Apr 01, 2015 (144)
27 HAMMER_LAB ss1794652615 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1918568946 Feb 12, 2016 (147)
29 HUMAN_LONGEVITY ss2164133563 Dec 20, 2016 (150)
30 TOPMED ss2326425810 Dec 20, 2016 (150)
31 ILLUMINA ss2632539974 Nov 08, 2017 (151)
32 GNOMAD ss2757366616 Nov 08, 2017 (151)
33 TOPMED ss3081742223 Nov 08, 2017 (151)
34 ILLUMINA ss3626140389 Oct 11, 2018 (152)
35 ILLUMINA ss3630574831 Oct 11, 2018 (152)
36 ILLUMINA ss3641600304 Oct 11, 2018 (152)
37 EVA_DECODE ss3687151880 Jul 12, 2019 (153)
38 KHV_HUMAN_GENOMES ss3799446984 Jul 12, 2019 (153)
39 EVA ss3826271647 Apr 25, 2020 (154)
40 SGDP_PRJ ss3849251188 Apr 25, 2020 (154)
41 TOPMED ss4456704843 Apr 25, 2021 (155)
42 1000Genomes NC_000001.10 - 83597067 Oct 11, 2018 (152)
43 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 83597067 Oct 11, 2018 (152)
44 Chileans NC_000001.10 - 83597067 Apr 25, 2020 (154)
45 gnomAD - Genomes NC_000001.11 - 83131384 Apr 25, 2021 (155)
46 HapMap NC_000001.11 - 83131384 Apr 25, 2020 (154)
47 Qatari NC_000001.10 - 83597067 Apr 25, 2020 (154)
48 SGDP_PRJ NC_000001.10 - 83597067 Apr 25, 2020 (154)
49 TopMed NC_000001.11 - 83131384 Apr 25, 2021 (155)
50 UK 10K study - Twins NC_000001.10 - 83597067 Oct 11, 2018 (152)
51 ALFA NC_000001.11 - 83131384 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)
rs60172464 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85945310, ss86165783 NC_000001.8:83309087:A:G NC_000001.11:83131383:A:G (self)
ss118850806, ss210573150, ss482416648, ss1584740011, ss1712348380 NC_000001.9:83369654:A:G NC_000001.11:83131383:A:G (self)
2417870, 1327233, 13839, 610876, 1268168, 1327233, ss218492057, ss480776508, ss533938728, ss554362551, ss779790337, ss781315417, ss835266183, ss1068043932, ss1291670591, ss1600583805, ss1643577838, ss1794652615, ss1918568946, ss2326425810, ss2632539974, ss2757366616, ss3626140389, ss3630574831, ss3641600304, ss3826271647, ss3849251188 NC_000001.10:83597066:A:G NC_000001.11:83131383:A:G (self)
17064975, 113062, 12793703, 20311178, 762077730, ss2164133563, ss3081742223, ss3687151880, ss3799446984, ss4456704843 NC_000001.11:83131383:A:G NC_000001.11:83131383:A:G (self)
ss13020154 NT_004902.14:465359:A:G NC_000001.11:83131383:A:G (self)
ss414356, ss595365, ss1023555, ss23145055, ss44072045, ss76843494, ss104815087 NT_032977.9:53568984:A:G NC_000001.11:83131383:A:G (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 rs323951

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.post596+ae089ad