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dbSNP Short Genetic Variations

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.

rs2820464

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:219519878 (GRCh38.p12) 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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.27579 (34631/125568, TOPMED)
A=0.2814 (8695/30902, GnomAD)
A=0.262 (1310/5008, 1000G) (+ 3 more)
A=0.348 (1560/4480, Estonian)
A=0.336 (1294/3854, ALSPAC)
A=0.328 (1215/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC102723886 : 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.p12 chr 1 NC_000001.11:g.219519878G>A
GRCh38.p12 chr 1 NC_000001.11:g.219519878G>C
GRCh37.p13 chr 1 NC_000001.10:g.219693220G>A
GRCh37.p13 chr 1 NC_000001.10:g.219693220G>C
Gene: LOC102723886, uncharacterized LOC102723886 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LYPLAL1-AS1 transcript NR_135822.1: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

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 125568 G=0.72421 A=0.27579
gnomAD - Genomes Global Study-wide 30902 G=0.7186 A=0.2814
gnomAD - Genomes European Sub 18460 G=0.6626 A=0.3374
gnomAD - Genomes African Sub 8704 G=0.855 A=0.145
gnomAD - Genomes East Asian Sub 1616 G=0.754 A=0.246
gnomAD - Genomes Other Sub 982 G=0.67 A=0.33
gnomAD - Genomes American Sub 838 G=0.51 A=0.49
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=0.76 A=0.24
1000Genomes Global Study-wide 5008 G=0.738 A=0.262
1000Genomes African Sub 1322 G=0.868 A=0.132
1000Genomes East Asian Sub 1008 G=0.749 A=0.251
1000Genomes Europe Sub 1006 G=0.677 A=0.323
1000Genomes South Asian Sub 978 G=0.78 A=0.22
1000Genomes American Sub 694 G=0.51 A=0.49
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.652 A=0.348
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.664 A=0.336
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.672 A=0.328
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 C Note
GRCh38.p12 chr 1 NC_000001.11:g.21...

NC_000001.11:g.219519878G=

NC_000001.11:g.21...

NC_000001.11:g.219519878G>A

NC_000001.11:g.21...

NC_000001.11:g.219519878G>C

GRCh37.p13 chr 1 NC_000001.10:g.21...

NC_000001.10:g.219693220G=

NC_000001.10:g.21...

NC_000001.10:g.219693220G>A

NC_000001.10:g.21...

NC_000001.10:g.219693220G>C

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#.

54 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3994239 Sep 28, 2001 (100)
2 WI_SSAHASNP ss6695208 Feb 20, 2003 (111)
3 SC_SNP ss13026280 Dec 05, 2003 (123)
4 CSHL-HAPMAP ss16392629 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss19101698 Feb 27, 2004 (120)
6 PERLEGEN ss24267524 Sep 20, 2004 (123)
7 ABI ss44042440 Mar 14, 2006 (126)
8 ILLUMINA ss65769413 Oct 14, 2006 (127)
9 AFFY ss76702443 Dec 07, 2007 (129)
10 BCMHGSC_JDW ss87976594 Mar 23, 2008 (129)
11 KRIBB_YJKIM ss104880848 Feb 04, 2009 (130)
12 BGI ss106633527 Feb 04, 2009 (130)
13 1000GENOMES ss108963736 Jan 23, 2009 (130)
14 ENSEMBL ss138157269 Dec 01, 2009 (131)
15 GMI ss156308740 Dec 01, 2009 (131)
16 ENSEMBL ss161219474 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss165824560 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss167517742 Jul 04, 2010 (132)
19 BUSHMAN ss199632974 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss205221966 Jul 04, 2010 (132)
21 1000GENOMES ss218892642 Jul 14, 2010 (132)
22 1000GENOMES ss230910729 Jul 14, 2010 (132)
23 1000GENOMES ss238520782 Jul 15, 2010 (132)
24 GMI ss276224227 May 04, 2012 (137)
25 PJP ss290738139 May 09, 2011 (134)
26 TISHKOFF ss555151156 Apr 25, 2013 (138)
27 SSMP ss648714812 Apr 25, 2013 (138)
28 EVA-GONL ss976165870 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1068617472 Aug 21, 2014 (142)
30 1000GENOMES ss1294727664 Aug 21, 2014 (142)
31 DDI ss1426118151 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1574693353 Apr 01, 2015 (144)
33 EVA_DECODE ss1585562428 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1602182343 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1645176376 Apr 01, 2015 (144)
36 EVA_SVP ss1712407017 Apr 01, 2015 (144)
37 WEILL_CORNELL_DGM ss1919388637 Feb 12, 2016 (147)
38 ILLUMINA ss1958358922 Feb 12, 2016 (147)
39 GENOMED ss1966978342 Jul 19, 2016 (147)
40 JJLAB ss2020217919 Sep 14, 2016 (149)
41 USC_VALOUEV ss2148248865 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2170251792 Dec 20, 2016 (150)
43 TOPMED ss2332872203 Dec 20, 2016 (150)
44 SYSTEMSBIOZJU ss2624618119 Nov 08, 2017 (151)
45 GRF ss2698242938 Nov 08, 2017 (151)
46 GNOMAD ss2766427450 Nov 08, 2017 (151)
47 AFFY ss2985539355 Nov 08, 2017 (151)
48 SWEGEN ss2988481694 Nov 08, 2017 (151)
49 ILLUMINA ss3021182188 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3023869185 Nov 08, 2017 (151)
51 TOPMED ss3103888311 Nov 08, 2017 (151)
52 TOPMED ss3103888312 Nov 08, 2017 (151)
53 CSHL ss3343920736 Nov 08, 2017 (151)
54 ILLUMINA ss3651527530 Oct 11, 2018 (152)
55 1000Genomes NC_000001.10 - 219693220 Oct 11, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 219693220 Oct 11, 2018 (152)
57 Genetic variation in the Estonian population NC_000001.10 - 219693220 Oct 11, 2018 (152)
58 gnomAD - Genomes NC_000001.10 - 219693220 Oct 11, 2018 (152)
59 TopMed NC_000001.11 - 219519878 Oct 11, 2018 (152)
60 UK 10K study - Twins NC_000001.10 - 219693220 Oct 11, 2018 (152)
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)
rs9431167 Sep 24, 2004 (123)
rs17543528 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss87976594, ss108963736, ss165824560, ss167517742, ss199632974, ss205221966, ss276224227, ss290738139, ss1585562428, ss1712407017 NC_000001.9:217759842:G:A NC_000001.11:219519877:G:A (self)
5584961, 3085377, 2181840, 15826649, 3085377, ss218892642, ss230910729, ss238520782, ss555151156, ss648714812, ss976165870, ss1068617472, ss1294727664, ss1426118151, ss1574693353, ss1602182343, ss1645176376, ss1919388637, ss1958358922, ss1966978342, ss2020217919, ss2148248865, ss2332872203, ss2624618119, ss2698242938, ss2766427450, ss2985539355, ss2988481694, ss3021182188, ss3343920736, ss3651527530 NC_000001.10:219693219:G:A NC_000001.11:219519877:G:A (self)
30073011, ss2170251792, ss3023869185, ss3103888311 NC_000001.11:219519877:G:A NC_000001.11:219519877:G:A (self)
ss16392629, ss19101698 NT_021877.16:13129125:G:A NC_000001.11:219519877:G:A (self)
ss13026280 NT_021953.15:786517:G:A NC_000001.11:219519877:G:A (self)
ss3994239, ss6695208, ss24267524, ss44042440, ss65769413, ss76702443, ss104880848, ss106633527, ss138157269, ss156308740, ss161219474 NT_167186.1:13210998:G:A NC_000001.11:219519877:G:A (self)
ss3103888312 NC_000001.11:219519877:G:C NC_000001.11:219519877:G:C (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 rs2820464

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.post104+4a6ee9c