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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.

rs201979697

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:155294540 (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
C=0.000030 (8/264690, TOPMED)
C=0.000048 (12/251228, GnomAD_exome)
C=0.000014 (2/140266, GnomAD) (+ 11 more)
C=0.000050 (6/121068, ExAC)
C=0.00000 (0/79454, ALFA)
C=0.00004 (3/78702, PAGE_STUDY)
C=0.00007 (2/28256, 14KJPN)
C=0.00012 (2/16760, 8.3KJPN)
C=0.0002 (1/6404, 1000G_30x)
C=0.0002 (1/5008, 1000G)
C=0.0014 (4/2922, KOREAN)
C=0.004 (3/792, PRJEB37584)
G=0.5 (1/2, SGDP_PRJ)
C=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PKLR : Missense 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 79454 G=1.00000 C=0.00000
European Sub 69364 G=1.00000 C=0.00000
African Sub 3698 G=1.0000 C=0.0000
African Others Sub 166 G=1.000 C=0.000
African American Sub 3532 G=1.0000 C=0.0000
Asian Sub 3274 G=1.0000 C=0.0000
East Asian Sub 2648 G=1.0000 C=0.0000
Other Asian Sub 626 G=1.000 C=0.000
Latin American 1 Sub 436 G=1.000 C=0.000
Latin American 2 Sub 928 G=1.000 C=0.000
South Asian Sub 274 G=1.000 C=0.000
Other Sub 1480 G=1.0000 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=0.999970 C=0.000030
gnomAD - Exomes Global Study-wide 251228 G=0.999952 C=0.000048
gnomAD - Exomes European Sub 135208 G=0.999993 C=0.000007
gnomAD - Exomes Asian Sub 49000 G=0.99978 C=0.00022
gnomAD - Exomes American Sub 34584 G=1.00000 C=0.00000
gnomAD - Exomes African Sub 16232 G=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10070 G=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6134 G=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 140266 G=0.999986 C=0.000014
gnomAD - Genomes European Sub 75950 G=1.00000 C=0.00000
gnomAD - Genomes African Sub 42050 G=1.00000 C=0.00000
gnomAD - Genomes American Sub 13658 G=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 G=0.9994 C=0.0006
gnomAD - Genomes Other Sub 2152 G=1.0000 C=0.0000
ExAC Global Study-wide 121068 G=0.999950 C=0.000050
ExAC Europe Sub 73180 G=1.00000 C=0.00000
ExAC Asian Sub 25132 G=0.99976 C=0.00024
ExAC American Sub 11548 G=1.00000 C=0.00000
ExAC African Sub 10300 G=1.00000 C=0.00000
ExAC Other Sub 908 G=1.000 C=0.000
Allele Frequency Aggregator Total Global 79454 G=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 69364 G=1.00000 C=0.00000
Allele Frequency Aggregator African Sub 3698 G=1.0000 C=0.0000
Allele Frequency Aggregator Asian Sub 3274 G=1.0000 C=0.0000
Allele Frequency Aggregator Other Sub 1480 G=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 928 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 436 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 274 G=1.000 C=0.000
The PAGE Study Global Study-wide 78702 G=0.99996 C=0.00004
The PAGE Study AfricanAmerican Sub 32516 G=1.00000 C=0.00000
The PAGE Study Mexican Sub 10810 G=1.00000 C=0.00000
The PAGE Study Asian Sub 8318 G=0.9996 C=0.0004
The PAGE Study PuertoRican Sub 7918 G=1.0000 C=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 C=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 C=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 C=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 C=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 C=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 C=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 C=0.000
14KJPN JAPANESE Study-wide 28256 G=0.99993 C=0.00007
8.3KJPN JAPANESE Study-wide 16760 G=0.99988 C=0.00012
1000Genomes_30x Global Study-wide 6404 G=0.9998 C=0.0002
1000Genomes_30x African Sub 1786 G=1.0000 C=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9991 C=0.0009
1000Genomes_30x American Sub 980 G=1.000 C=0.000
1000Genomes Global Study-wide 5008 G=0.9998 C=0.0002
1000Genomes African Sub 1322 G=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 C=0.0010
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=1.000 C=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9986 C=0.0014
CNV burdens in cranial meningiomas Global Study-wide 792 G=0.996 C=0.004
CNV burdens in cranial meningiomas CRM Sub 792 G=0.996 C=0.004
SGDP_PRJ Global Study-wide 2 G=0.5 C=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 1 NC_000001.11:g.155294540G>A
GRCh38.p14 chr 1 NC_000001.11:g.155294540G>C
GRCh37.p13 chr 1 NC_000001.10:g.155264331G>A
GRCh37.p13 chr 1 NC_000001.10:g.155264331G>C
PKLR RefSeqGene (LRG_1136) NG_011677.1:g.11895C>T
PKLR RefSeqGene (LRG_1136) NG_011677.1:g.11895C>G
GRCh38.p14 chr 1 alt locus HSCHR1_2_CTG31 NW_003315906.1:g.99563G>A
GRCh38.p14 chr 1 alt locus HSCHR1_2_CTG31 NW_003315906.1:g.99563G>C
Gene: PKLR, pyruvate kinase L/R (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PKLR transcript variant 1 NM_000298.6:c.907C>T P [CCG] > S [TCG] Coding Sequence Variant
pyruvate kinase PKLR isoform 1 NP_000289.1:p.Pro303Ser P (Pro) > S (Ser) Missense Variant
PKLR transcript variant 1 NM_000298.6:c.907C>G P [CCG] > A [GCG] Coding Sequence Variant
pyruvate kinase PKLR isoform 1 NP_000289.1:p.Pro303Ala P (Pro) > A (Ala) Missense Variant
PKLR transcript variant 2 NM_181871.4:c.814C>T P [CCG] > S [TCG] Coding Sequence Variant
pyruvate kinase PKLR isoform 2 NP_870986.1:p.Pro272Ser P (Pro) > S (Ser) Missense Variant
PKLR transcript variant 2 NM_181871.4:c.814C>G P [CCG] > A [GCG] Coding Sequence Variant
pyruvate kinase PKLR isoform 2 NP_870986.1:p.Pro272Ala P (Pro) > A (Ala) Missense Variant
PKLR transcript variant X5 XM_017001493.1:c.907C>T P [CCG] > S [TCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X3 XP_016856982.1:p.Pro303Ser P (Pro) > S (Ser) Missense Variant
PKLR transcript variant X5 XM_017001493.1:c.907C>G P [CCG] > A [GCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X3 XP_016856982.1:p.Pro303Ala P (Pro) > A (Ala) Missense Variant
PKLR transcript variant X1 XM_047422591.1:c.907C>T P [CCG] > S [TCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X1 XP_047278547.1:p.Pro303Ser P (Pro) > S (Ser) Missense Variant
PKLR transcript variant X1 XM_047422591.1:c.907C>G P [CCG] > A [GCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X1 XP_047278547.1:p.Pro303Ala P (Pro) > A (Ala) Missense Variant
PKLR transcript variant X2 XM_047422592.1:c.907C>T P [CCG] > S [TCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X1 XP_047278548.1:p.Pro303Ser P (Pro) > S (Ser) Missense Variant
PKLR transcript variant X2 XM_047422592.1:c.907C>G P [CCG] > A [GCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X1 XP_047278548.1:p.Pro303Ala P (Pro) > A (Ala) Missense Variant
PKLR transcript variant X3 XM_011509640.4:c.715C>T P [CCG] > S [TCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X2 XP_011507942.1:p.Pro239Ser P (Pro) > S (Ser) Missense Variant
PKLR transcript variant X3 XM_011509640.4:c.715C>G P [CCG] > A [GCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X2 XP_011507942.1:p.Pro239Ala P (Pro) > A (Ala) Missense Variant
PKLR transcript variant X4 XM_006711386.5:c.715C>T P [CCG] > S [TCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X2 XP_006711449.1:p.Pro239Ser P (Pro) > S (Ser) Missense Variant
PKLR transcript variant X4 XM_006711386.5:c.715C>G P [CCG] > A [GCG] Coding Sequence Variant
pyruvate kinase PKLR isoform X2 XP_006711449.1:p.Pro239Ala P (Pro) > A (Ala) Missense 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.155294540= NC_000001.11:g.155294540G>A NC_000001.11:g.155294540G>C
GRCh37.p13 chr 1 NC_000001.10:g.155264331= NC_000001.10:g.155264331G>A NC_000001.10:g.155264331G>C
PKLR RefSeqGene (LRG_1136) NG_011677.1:g.11895= NG_011677.1:g.11895C>T NG_011677.1:g.11895C>G
PKLR transcript variant 1 NM_000298.6:c.907= NM_000298.6:c.907C>T NM_000298.6:c.907C>G
PKLR transcript variant 1 NM_000298.5:c.907= NM_000298.5:c.907C>T NM_000298.5:c.907C>G
PKLR transcript variant 2 NM_181871.4:c.814= NM_181871.4:c.814C>T NM_181871.4:c.814C>G
PKLR transcript variant 2 NM_181871.3:c.814= NM_181871.3:c.814C>T NM_181871.3:c.814C>G
GRCh38.p14 chr 1 alt locus HSCHR1_2_CTG31 NW_003315906.1:g.99563= NW_003315906.1:g.99563G>A NW_003315906.1:g.99563G>C
PKLR transcript variant X4 XM_006711386.5:c.715= XM_006711386.5:c.715C>T XM_006711386.5:c.715C>G
PKLR transcript variant X1 XM_006711386.4:c.715= XM_006711386.4:c.715C>T XM_006711386.4:c.715C>G
PKLR transcript variant X1 XM_006711386.3:c.715= XM_006711386.3:c.715C>T XM_006711386.3:c.715C>G
PKLR transcript variant X3 XM_006711386.2:c.715= XM_006711386.2:c.715C>T XM_006711386.2:c.715C>G
PKLR transcript variant X2 XM_006711386.1:c.715= XM_006711386.1:c.715C>T XM_006711386.1:c.715C>G
PKLR transcript variant X2 XM_047422592.1:c.907= XM_047422592.1:c.907C>T XM_047422592.1:c.907C>G
PKLR transcript variant X3 XM_011509640.4:c.715= XM_011509640.4:c.715C>T XM_011509640.4:c.715C>G
PKLR transcript variant X3 XM_011509640.3:c.715= XM_011509640.3:c.715C>T XM_011509640.3:c.715C>G
PKLR transcript variant X3 XM_011509640.2:c.715= XM_011509640.2:c.715C>T XM_011509640.2:c.715C>G
PKLR transcript variant X5 XM_011509640.1:c.715= XM_011509640.1:c.715C>T XM_011509640.1:c.715C>G
PKLR transcript variant X1 XM_047422591.1:c.907= XM_047422591.1:c.907C>T XM_047422591.1:c.907C>G
PKLR transcript variant X5 XM_017001493.1:c.907= XM_017001493.1:c.907C>T XM_017001493.1:c.907C>G
pyruvate kinase PKLR isoform 1 NP_000289.1:p.Pro303= NP_000289.1:p.Pro303Ser NP_000289.1:p.Pro303Ala
pyruvate kinase PKLR isoform 2 NP_870986.1:p.Pro272= NP_870986.1:p.Pro272Ser NP_870986.1:p.Pro272Ala
pyruvate kinase PKLR isoform X2 XP_006711449.1:p.Pro239= XP_006711449.1:p.Pro239Ser XP_006711449.1:p.Pro239Ala
pyruvate kinase PKLR isoform X1 XP_047278548.1:p.Pro303= XP_047278548.1:p.Pro303Ser XP_047278548.1:p.Pro303Ala
pyruvate kinase PKLR isoform X2 XP_011507942.1:p.Pro239= XP_011507942.1:p.Pro239Ser XP_011507942.1:p.Pro239Ala
pyruvate kinase PKLR isoform X1 XP_047278547.1:p.Pro303= XP_047278547.1:p.Pro303Ser XP_047278547.1:p.Pro303Ala
pyruvate kinase PKLR isoform X3 XP_016856982.1:p.Pro303= XP_016856982.1:p.Pro303Ser XP_016856982.1:p.Pro303Ala
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, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488685100 May 04, 2012 (137)
2 EXOME_CHIP ss491302693 May 04, 2012 (137)
3 ILLUMINA ss780802829 Sep 08, 2015 (146)
4 ILLUMINA ss783484309 Sep 08, 2015 (146)
5 1000GENOMES ss1292943665 Aug 21, 2014 (142)
6 EVA_EXAC ss1685818288 Apr 01, 2015 (144)
7 ILLUMINA ss1751872802 Sep 08, 2015 (146)
8 ILLUMINA ss1917735633 Feb 12, 2016 (147)
9 ILLUMINA ss1946009925 Feb 12, 2016 (147)
10 ILLUMINA ss1958318634 Feb 12, 2016 (147)
11 GNOMAD ss2731912640 Nov 08, 2017 (151)
12 GNOMAD ss2746456442 Nov 08, 2017 (151)
13 GNOMAD ss2761370613 Nov 08, 2017 (151)
14 AFFY ss2984879823 Nov 08, 2017 (151)
15 ILLUMINA ss3021137304 Nov 08, 2017 (151)
16 ILLUMINA ss3625550948 Oct 11, 2018 (152)
17 ILLUMINA ss3626209917 Oct 11, 2018 (152)
18 ILLUMINA ss3634350460 Oct 11, 2018 (152)
19 ILLUMINA ss3640057815 Oct 11, 2018 (152)
20 BUMPUSLAB ss3644051369 Oct 11, 2018 (152)
21 ILLUMINA ss3644505882 Oct 11, 2018 (152)
22 ILLUMINA ss3651471836 Oct 11, 2018 (152)
23 ILLUMINA ss3653649037 Oct 11, 2018 (152)
24 ILLUMINA ss3725066338 Jul 12, 2019 (153)
25 ILLUMINA ss3744352889 Jul 12, 2019 (153)
26 ILLUMINA ss3744651362 Jul 12, 2019 (153)
27 EVA ss3746813635 Jul 12, 2019 (153)
28 PAGE_CC ss3770841711 Jul 12, 2019 (153)
29 ILLUMINA ss3772152483 Jul 12, 2019 (153)
30 SGDP_PRJ ss3850015234 Apr 25, 2020 (154)
31 KRGDB ss3895224480 Apr 25, 2020 (154)
32 EVA ss3984464866 Apr 25, 2021 (155)
33 TOPMED ss4468473467 Apr 25, 2021 (155)
34 TOMMO_GENOMICS ss5146505848 Apr 25, 2021 (155)
35 EVA ss5236873894 Apr 25, 2021 (155)
36 EVA ss5322079720 Oct 17, 2022 (156)
37 1000G_HIGH_COVERAGE ss5517644873 Oct 17, 2022 (156)
38 TOMMO_GENOMICS ss5673709121 Oct 17, 2022 (156)
39 EVA ss5847556860 Oct 17, 2022 (156)
40 EVA ss5910263173 Oct 17, 2022 (156)
41 EVA ss5938394011 Oct 17, 2022 (156)
42 1000Genomes NC_000001.10 - 155264331 Oct 11, 2018 (152)
43 1000Genomes_30x NC_000001.11 - 155294540 Oct 17, 2022 (156)
44 ExAC NC_000001.10 - 155264331 Oct 11, 2018 (152)
45 gnomAD - Genomes NC_000001.11 - 155294540 Apr 25, 2021 (155)
46 gnomAD - Exomes NC_000001.10 - 155264331 Jul 12, 2019 (153)
47 KOREAN population from KRGDB NC_000001.10 - 155264331 Apr 25, 2020 (154)
48 The PAGE Study NC_000001.11 - 155294540 Jul 12, 2019 (153)
49 CNV burdens in cranial meningiomas NC_000001.10 - 155264331 Apr 25, 2021 (155)
50 SGDP_PRJ NC_000001.10 - 155264331 Apr 25, 2020 (154)
51 8.3KJPN NC_000001.10 - 155264331 Apr 25, 2021 (155)
52 14KJPN NC_000001.11 - 155294540 Oct 17, 2022 (156)
53 TopMed NC_000001.11 - 155294540 Apr 25, 2021 (155)
54 ALFA NC_000001.11 - 155294540 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3644051369 NC_000001.10:155264330:G:A NC_000001.11:155294539:G:A (self)
3736297, 5037826, 935754, 2401874, 14181, 2032214, 4475155, ss488685100, ss491302693, ss780802829, ss783484309, ss1292943665, ss1685818288, ss1751872802, ss1917735633, ss1946009925, ss1958318634, ss2731912640, ss2746456442, ss2761370613, ss2984879823, ss3021137304, ss3625550948, ss3626209917, ss3634350460, ss3640057815, ss3644505882, ss3651471836, ss3653649037, ss3744352889, ss3744651362, ss3746813635, ss3772152483, ss3850015234, ss3895224480, ss3984464866, ss5146505848, ss5322079720, ss5847556860, ss5938394011 NC_000001.10:155264330:G:C NC_000001.11:155294539:G:C (self)
5170808, 27192722, 63180, 7546225, 32079802, 7114739199, ss3725066338, ss3770841711, ss4468473467, ss5236873894, ss5517644873, ss5673709121, ss5910263173 NC_000001.11:155294539:G:C NC_000001.11:155294539: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 rs201979697

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