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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.

rs2820464

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:219519878 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.284336 (75261/264690, TOPMED)
A=0.27745 (21835/78698, PAGE_STUDY)
A=0.36212 (10232/28256, 14KJPN) (+ 18 more)
A=0.23741 (4497/18942, ALFA)
A=0.35722 (5987/16760, 8.3KJPN)
A=0.2639 (1690/6404, 1000G_30x)
A=0.2616 (1310/5008, 1000G)
A=0.3482 (1560/4480, Estonian)
A=0.3358 (1294/3854, ALSPAC)
A=0.3277 (1215/3708, TWINSUK)
A=0.3229 (946/2930, KOREAN)
A=0.2466 (465/1886, HapMap)
A=0.323 (322/998, GoNL)
A=0.312 (244/782, PRJEB37584)
A=0.338 (203/600, NorthernSweden)
G=0.360 (93/258, SGDP_PRJ)
A=0.296 (64/216, Qatari)
A=0.196 (42/214, Vietnamese)
A=0.19 (12/62, Ancient Sardinia)
G=0.27 (12/44, Siberian)
A=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LYPLAL1-AS1 : 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 18942 G=0.76259 A=0.23741, C=0.00000
European Sub 11526 G=0.75941 A=0.24059, C=0.00000
African Sub 3330 G=0.9492 A=0.0508, C=0.0000
African Others Sub 106 G=0.981 A=0.019, C=0.000
African American Sub 3224 G=0.9482 A=0.0518, C=0.0000
Asian Sub 148 G=0.872 A=0.128, C=0.000
East Asian Sub 104 G=0.846 A=0.154, C=0.000
Other Asian Sub 44 G=0.93 A=0.07, C=0.00
Latin American 1 Sub 224 G=0.763 A=0.237, C=0.000
Latin American 2 Sub 2328 G=0.5541 A=0.4459, C=0.0000
South Asian Sub 78 G=0.90 A=0.10, C=0.00
Other Sub 1308 G=0.6659 A=0.3341, C=0.0000


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=0.715664 A=0.284336
The PAGE Study Global Study-wide 78698 G=0.72255 A=0.27745
The PAGE Study AfricanAmerican Sub 32512 G=0.85067 A=0.14933
The PAGE Study Mexican Sub 10810 G=0.49223 A=0.50777
The PAGE Study Asian Sub 8318 G=0.6669 A=0.3331
The PAGE Study PuertoRican Sub 7918 G=0.6570 A=0.3430
The PAGE Study NativeHawaiian Sub 4534 G=0.8114 A=0.1886
The PAGE Study Cuban Sub 4230 G=0.6868 A=0.3132
The PAGE Study Dominican Sub 3828 G=0.7390 A=0.2610
The PAGE Study CentralAmerican Sub 2450 G=0.5204 A=0.4796
The PAGE Study SouthAmerican Sub 1982 G=0.4879 A=0.5121
The PAGE Study NativeAmerican Sub 1260 G=0.6714 A=0.3286
The PAGE Study SouthAsian Sub 856 G=0.742 A=0.258
14KJPN JAPANESE Study-wide 28256 G=0.63788 A=0.36212
Allele Frequency Aggregator Total Global 18942 G=0.76259 A=0.23741, C=0.00000
Allele Frequency Aggregator European Sub 11526 G=0.75941 A=0.24059, C=0.00000
Allele Frequency Aggregator African Sub 3330 G=0.9492 A=0.0508, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 2328 G=0.5541 A=0.4459, C=0.0000
Allele Frequency Aggregator Other Sub 1308 G=0.6659 A=0.3341, C=0.0000
Allele Frequency Aggregator Latin American 1 Sub 224 G=0.763 A=0.237, C=0.000
Allele Frequency Aggregator Asian Sub 148 G=0.872 A=0.128, C=0.000
Allele Frequency Aggregator South Asian Sub 78 G=0.90 A=0.10, C=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.64278 A=0.35722
1000Genomes_30x Global Study-wide 6404 G=0.7361 A=0.2639
1000Genomes_30x African Sub 1786 G=0.8723 A=0.1277
1000Genomes_30x Europe Sub 1266 G=0.6706 A=0.3294
1000Genomes_30x South Asian Sub 1202 G=0.7737 A=0.2263
1000Genomes_30x East Asian Sub 1170 G=0.7530 A=0.2470
1000Genomes_30x American Sub 980 G=0.506 A=0.494
1000Genomes Global Study-wide 5008 G=0.7384 A=0.2616
1000Genomes African Sub 1322 G=0.8684 A=0.1316
1000Genomes East Asian Sub 1008 G=0.7490 A=0.2510
1000Genomes Europe Sub 1006 G=0.6769 A=0.3231
1000Genomes South Asian Sub 978 G=0.777 A=0.223
1000Genomes American Sub 694 G=0.510 A=0.490
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6518 A=0.3482
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6642 A=0.3358
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6723 A=0.3277
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6771 A=0.3229
HapMap Global Study-wide 1886 G=0.7534 A=0.2466
HapMap American Sub 764 G=0.702 A=0.298
HapMap African Sub 692 G=0.858 A=0.142
HapMap Asian Sub 254 G=0.689 A=0.311
HapMap Europe Sub 176 G=0.659 A=0.341
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.677 A=0.323
CNV burdens in cranial meningiomas Global Study-wide 782 G=0.688 A=0.312
CNV burdens in cranial meningiomas CRM Sub 782 G=0.688 A=0.312
Northern Sweden ACPOP Study-wide 600 G=0.662 A=0.338
SGDP_PRJ Global Study-wide 258 G=0.360 A=0.640
Qatari Global Study-wide 216 G=0.704 A=0.296
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.804 A=0.196
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 62 G=0.81 A=0.19
Siberian Global Study-wide 44 G=0.27 A=0.73
The Danish reference pan genome Danish Study-wide 40 G=0.62 A=0.38
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.219519878G>A
GRCh38.p14 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: LYPLAL1-AS1, LYPLAL1 antisense RNA 1 (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

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
GRCh38.p14 chr 1 NC_000001.11:g.219519878= NC_000001.11:g.219519878G>A NC_000001.11:g.219519878G>C
GRCh37.p13 chr 1 NC_000001.10:g.219693220= NC_000001.10:g.219693220G>A 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#.

82 SubSNP, 23 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 SYSTEMSBIOZJU ss2624618119 Nov 08, 2017 (151)
44 GRF ss2698242938 Nov 08, 2017 (151)
45 GNOMAD ss2766427450 Nov 08, 2017 (151)
46 AFFY ss2985539355 Nov 08, 2017 (151)
47 SWEGEN ss2988481694 Nov 08, 2017 (151)
48 ILLUMINA ss3021182188 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3023869185 Nov 08, 2017 (151)
50 CSHL ss3343920736 Nov 08, 2017 (151)
51 ILLUMINA ss3651527530 Oct 11, 2018 (152)
52 EGCUT_WGS ss3656443592 Jul 12, 2019 (153)
53 EVA_DECODE ss3688667022 Jul 12, 2019 (153)
54 ILLUMINA ss3725107539 Jul 12, 2019 (153)
55 ACPOP ss3727879915 Jul 12, 2019 (153)
56 EVA ss3747359110 Jul 12, 2019 (153)
57 PAGE_CC ss3770873407 Jul 12, 2019 (153)
58 KHV_HUMAN_GENOMES ss3800362869 Jul 12, 2019 (153)
59 EVA ss3826653603 Apr 25, 2020 (154)
60 EVA ss3836727592 Apr 25, 2020 (154)
61 EVA ss3842139548 Apr 25, 2020 (154)
62 SGDP_PRJ ss3850936533 Apr 25, 2020 (154)
63 KRGDB ss3896254514 Apr 25, 2020 (154)
64 EVA ss3984472327 Apr 25, 2021 (155)
65 EVA ss3984853354 Apr 25, 2021 (155)
66 TOPMED ss4484250662 Apr 25, 2021 (155)
67 TOMMO_GENOMICS ss5148514379 Apr 25, 2021 (155)
68 1000G_HIGH_COVERAGE ss5245861891 Oct 13, 2022 (156)
69 HUGCELL_USP ss5446295167 Oct 13, 2022 (156)
70 EVA ss5506193671 Oct 13, 2022 (156)
71 1000G_HIGH_COVERAGE ss5519996228 Oct 13, 2022 (156)
72 SANFORD_IMAGENETICS ss5624230510 Oct 13, 2022 (156)
73 SANFORD_IMAGENETICS ss5627486335 Oct 13, 2022 (156)
74 TOMMO_GENOMICS ss5676298115 Oct 13, 2022 (156)
75 YY_MCH ss5801653535 Oct 13, 2022 (156)
76 EVA ss5833288019 Oct 13, 2022 (156)
77 EVA ss5847174914 Oct 13, 2022 (156)
78 EVA ss5847574794 Oct 13, 2022 (156)
79 EVA ss5849293042 Oct 13, 2022 (156)
80 EVA ss5912053895 Oct 13, 2022 (156)
81 EVA ss5939326739 Oct 13, 2022 (156)
82 EVA ss5979305640 Oct 13, 2022 (156)
83 1000Genomes NC_000001.10 - 219693220 Oct 11, 2018 (152)
84 1000Genomes_30x NC_000001.11 - 219519878 Oct 13, 2022 (156)
85 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 219693220 Oct 11, 2018 (152)
86 Genetic variation in the Estonian population NC_000001.10 - 219693220 Oct 11, 2018 (152)
87 The Danish reference pan genome NC_000001.10 - 219693220 Apr 25, 2020 (154)
88 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 40126577 (NC_000001.11:219519877:G:A 38897/139926)
Row 40126578 (NC_000001.11:219519877:G:C 1/139974)

- Apr 25, 2021 (155)
89 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 40126577 (NC_000001.11:219519877:G:A 38897/139926)
Row 40126578 (NC_000001.11:219519877:G:C 1/139974)

- Apr 25, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000001.10 - 219693220 Apr 25, 2020 (154)
91 HapMap NC_000001.11 - 219519878 Apr 25, 2020 (154)
92 KOREAN population from KRGDB NC_000001.10 - 219693220 Apr 25, 2020 (154)
93 Northern Sweden NC_000001.10 - 219693220 Jul 12, 2019 (153)
94 The PAGE Study NC_000001.11 - 219519878 Jul 12, 2019 (153)
95 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 219693220 Apr 25, 2021 (155)
96 CNV burdens in cranial meningiomas NC_000001.10 - 219693220 Apr 25, 2021 (155)
97 Qatari NC_000001.10 - 219693220 Apr 25, 2020 (154)
98 SGDP_PRJ NC_000001.10 - 219693220 Apr 25, 2020 (154)
99 Siberian NC_000001.10 - 219693220 Apr 25, 2020 (154)
100 8.3KJPN NC_000001.10 - 219693220 Apr 25, 2021 (155)
101 14KJPN NC_000001.11 - 219519878 Oct 13, 2022 (156)
102 TopMed NC_000001.11 - 219519878 Apr 25, 2021 (155)
103 UK 10K study - Twins NC_000001.10 - 219693220 Oct 11, 2018 (152)
104 A Vietnamese Genetic Variation Database NC_000001.10 - 219693220 Jul 12, 2019 (153)
105 ALFA NC_000001.11 - 219519878 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)
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, 1893221, 1348754, 3431908, 1164780, 79281, 21648, 1430567, 2953513, 765219, 6483686, 3085377, 668626, ss218892642, ss230910729, ss238520782, ss555151156, ss648714812, ss976165870, ss1068617472, ss1294727664, ss1426118151, ss1574693353, ss1602182343, ss1645176376, ss1919388637, ss1958358922, ss1966978342, ss2020217919, ss2148248865, ss2624618119, ss2698242938, ss2766427450, ss2985539355, ss2988481694, ss3021182188, ss3343920736, ss3651527530, ss3656443592, ss3727879915, ss3747359110, ss3826653603, ss3836727592, ss3850936533, ss3896254514, ss3984472327, ss3984853354, ss5148514379, ss5506193671, ss5624230510, ss5627486335, ss5833288019, ss5847174914, ss5847574794, ss5939326739, ss5979305640 NC_000001.10:219693219:G:A NC_000001.11:219519877:G:A (self)
7522163, 273529, 94876, 10135219, 47856997, 12809778979, ss2170251792, ss3023869185, ss3688667022, ss3725107539, ss3770873407, ss3800362869, ss3842139548, ss4484250662, ss5245861891, ss5446295167, ss5519996228, ss5676298115, ss5801653535, ss5849293042, ss5912053895 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)
12809778979 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

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