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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.

rs132979

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:38166917 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.120586 (31918/264690, TOPMED)
T=0.115492 (16167/139984, GnomAD)
T=0.09523 (1809/18996, ALFA) (+ 15 more)
T=0.09200 (1542/16760, 8.3KJPN)
T=0.1308 (655/5008, 1000G)
T=0.0527 (236/4480, Estonian)
T=0.0916 (353/3854, ALSPAC)
T=0.0887 (329/3708, TWINSUK)
T=0.1020 (298/2922, KOREAN)
T=0.113 (113/998, GoNL)
T=0.095 (57/600, NorthernSweden)
T=0.140 (46/328, HapMap)
T=0.125 (27/216, Qatari)
T=0.132 (28/212, Vietnamese)
C=0.442 (46/104, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PLA2G6 : 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 22 NC_000022.11:g.38166917C>T
GRCh37.p13 chr 22 NC_000022.10:g.38562924C>T
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.52862G>A
PLA2G6 RefSeqGene NG_007094.2:g.43774G>A
Gene: PLA2G6, phospholipase A2 group VI (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PLA2G6 transcript variant 2 NM_001004426.3:c.209+2301…

NM_001004426.3:c.209+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 3 NM_001199562.3:c.209+2301…

NM_001199562.3:c.209+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 4 NM_001349864.2:c.209+2301…

NM_001349864.2:c.209+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 5 NM_001349865.2:c.209+2301…

NM_001349865.2:c.209+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 6 NM_001349866.2:c.209+2301…

NM_001349866.2:c.209+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+230…

NM_001349867.2:c.-457+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+230…

NM_001349868.2:c.-282+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+230…

NM_001349869.2:c.-457+2301G>A

N/A Intron Variant
PLA2G6 transcript variant 1 NM_003560.4:c.209+2301G>A 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 18996 C=0.90477 T=0.09523
European Sub 14370 C=0.91921 T=0.08079
African Sub 2950 C=0.8349 T=0.1651
African Others Sub 114 C=0.816 T=0.184
African American Sub 2836 C=0.8357 T=0.1643
Asian Sub 114 C=0.851 T=0.149
East Asian Sub 88 C=0.84 T=0.16
Other Asian Sub 26 C=0.88 T=0.12
Latin American 1 Sub 146 C=0.918 T=0.082
Latin American 2 Sub 610 C=0.926 T=0.074
South Asian Sub 100 C=0.87 T=0.13
Other Sub 706 C=0.895 T=0.105


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 C=0.879414 T=0.120586
gnomAD - Genomes Global Study-wide 139984 C=0.884508 T=0.115492
gnomAD - Genomes European Sub 75852 C=0.91370 T=0.08630
gnomAD - Genomes African Sub 41924 C=0.82258 T=0.17742
gnomAD - Genomes American Sub 13618 C=0.91849 T=0.08151
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.8865 T=0.1135
gnomAD - Genomes East Asian Sub 3128 C=0.8545 T=0.1455
gnomAD - Genomes Other Sub 2140 C=0.8874 T=0.1126
8.3KJPN JAPANESE Study-wide 16760 C=0.90800 T=0.09200
1000Genomes Global Study-wide 5008 C=0.8692 T=0.1308
1000Genomes African Sub 1322 C=0.8245 T=0.1755
1000Genomes East Asian Sub 1008 C=0.8641 T=0.1359
1000Genomes Europe Sub 1006 C=0.9036 T=0.0964
1000Genomes South Asian Sub 978 C=0.859 T=0.141
1000Genomes American Sub 694 C=0.927 T=0.073
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9473 T=0.0527
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9084 T=0.0916
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9113 T=0.0887
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.8980 T=0.1020
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.887 T=0.113
Northern Sweden ACPOP Study-wide 600 C=0.905 T=0.095
HapMap Global Study-wide 328 C=0.860 T=0.140
HapMap African Sub 120 C=0.792 T=0.208
HapMap American Sub 120 C=0.883 T=0.117
HapMap Asian Sub 88 C=0.92 T=0.08
Qatari Global Study-wide 216 C=0.875 T=0.125
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.868 T=0.132
SGDP_PRJ Global Study-wide 104 C=0.442 T=0.558
The Danish reference pan genome Danish Study-wide 40 C=0.85 T=0.15
Siberian Global Study-wide 4 C=0.5 T=0.5
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 C= T
GRCh38.p13 chr 22 NC_000022.11:g.38166917= NC_000022.11:g.38166917C>T
GRCh37.p13 chr 22 NC_000022.10:g.38562924= NC_000022.10:g.38562924C>T
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.52862= NG_007094.3:g.52862G>A
PLA2G6 RefSeqGene NG_007094.2:g.43774= NG_007094.2:g.43774G>A
PLA2G6 transcript variant 2 NM_001004426.1:c.209+2301= NM_001004426.1:c.209+2301G>A
PLA2G6 transcript variant 2 NM_001004426.3:c.209+2301= NM_001004426.3:c.209+2301G>A
PLA2G6 transcript variant 3 NM_001199562.1:c.209+2301= NM_001199562.1:c.209+2301G>A
PLA2G6 transcript variant 3 NM_001199562.3:c.209+2301= NM_001199562.3:c.209+2301G>A
PLA2G6 transcript variant 4 NM_001349864.2:c.209+2301= NM_001349864.2:c.209+2301G>A
PLA2G6 transcript variant 5 NM_001349865.2:c.209+2301= NM_001349865.2:c.209+2301G>A
PLA2G6 transcript variant 6 NM_001349866.2:c.209+2301= NM_001349866.2:c.209+2301G>A
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+2301= NM_001349867.2:c.-457+2301G>A
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+2301= NM_001349868.2:c.-282+2301G>A
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+2301= NM_001349869.2:c.-457+2301G>A
PLA2G6 transcript variant 1 NM_003560.2:c.209+2301= NM_003560.2:c.209+2301G>A
PLA2G6 transcript variant 1 NM_003560.4:c.209+2301= NM_003560.4:c.209+2301G>A
PLA2G6 transcript variant X1 XM_005261764.1:c.209+2301= XM_005261764.1:c.209+2301G>A
PLA2G6 transcript variant X3 XM_005261765.1:c.209+2301= XM_005261765.1:c.209+2301G>A
PLA2G6 transcript variant X2 XM_005261766.1:c.209+2301= XM_005261766.1:c.209+2301G>A
PLA2G6 transcript variant X4 XM_005261767.1:c.209+2301= XM_005261767.1:c.209+2301G>A
PLA2G6 transcript variant X5 XM_005261768.1:c.209+2301= XM_005261768.1:c.209+2301G>A
PLA2G6 transcript variant X6 XM_005261769.1:c.209+2301= XM_005261769.1:c.209+2301G>A
PLA2G6 transcript variant X7 XM_005261770.1:c.-282+2301= XM_005261770.1:c.-282+2301G>A
PLA2G6 transcript variant X8 XM_005261771.1:c.209+2301= XM_005261771.1:c.209+2301G>A
PLA2G6 transcript variant X9 XM_005261772.1:c.209+2301= XM_005261772.1:c.209+2301G>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#.

42 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC ss140787 Jun 24, 2000 (78)
2 KRIBB_YJKIM ss80750543 Dec 15, 2007 (130)
3 ILLUMINA-UK ss117408537 Dec 01, 2009 (131)
4 BCM-HGSC-SUB ss208838932 Jul 04, 2010 (132)
5 1000GENOMES ss228687289 Jul 14, 2010 (132)
6 1000GENOMES ss238074440 Jul 15, 2010 (132)
7 1000GENOMES ss244191244 Jul 15, 2010 (132)
8 GMI ss283640620 May 04, 2012 (137)
9 GMI ss287571477 Apr 25, 2013 (138)
10 TISHKOFF ss566650881 Apr 25, 2013 (138)
11 SSMP ss662579988 Apr 25, 2013 (138)
12 EVA-GONL ss995367235 Aug 21, 2014 (142)
13 JMKIDD_LAB ss1082669844 Aug 21, 2014 (142)
14 1000GENOMES ss1367226463 Aug 21, 2014 (142)
15 DDI ss1429261232 Apr 01, 2015 (144)
16 EVA_GENOME_DK ss1579758790 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1640026796 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1683020829 Apr 01, 2015 (144)
19 EVA_DECODE ss1699438013 Apr 01, 2015 (144)
20 HAMMER_LAB ss1809795962 Sep 08, 2015 (146)
21 WEILL_CORNELL_DGM ss1938934768 Feb 12, 2016 (147)
22 JJLAB ss2030239374 Sep 14, 2016 (149)
23 USC_VALOUEV ss2158858959 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2247456825 Dec 20, 2016 (150)
25 TOPMED ss2414424221 Dec 20, 2016 (150)
26 GRF ss2704611035 Nov 08, 2017 (151)
27 GNOMAD ss2974556926 Nov 08, 2017 (151)
28 SWEGEN ss3019329269 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3028956882 Nov 08, 2017 (151)
30 CSHL ss3352845045 Nov 08, 2017 (151)
31 TOPMED ss3377567412 Nov 08, 2017 (151)
32 EGCUT_WGS ss3685824554 Jul 13, 2019 (153)
33 EVA_DECODE ss3708232379 Jul 13, 2019 (153)
34 ACPOP ss3743947573 Jul 13, 2019 (153)
35 EVA ss3759402508 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3822564829 Jul 13, 2019 (153)
37 EVA ss3841628398 Apr 27, 2020 (154)
38 EVA ss3847143522 Apr 27, 2020 (154)
39 SGDP_PRJ ss3890579715 Apr 27, 2020 (154)
40 KRGDB ss3940981711 Apr 27, 2020 (154)
41 TOPMED ss5109746090 Apr 27, 2021 (155)
42 TOMMO_GENOMICS ss5232698410 Apr 27, 2021 (155)
43 1000Genomes NC_000022.10 - 38562924 Oct 12, 2018 (152)
44 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 38562924 Oct 12, 2018 (152)
45 Genetic variation in the Estonian population NC_000022.10 - 38562924 Oct 12, 2018 (152)
46 The Danish reference pan genome NC_000022.10 - 38562924 Apr 27, 2020 (154)
47 gnomAD - Genomes NC_000022.11 - 38166917 Apr 27, 2021 (155)
48 Genome of the Netherlands Release 5 NC_000022.10 - 38562924 Apr 27, 2020 (154)
49 HapMap NC_000022.11 - 38166917 Apr 27, 2020 (154)
50 KOREAN population from KRGDB NC_000022.10 - 38562924 Apr 27, 2020 (154)
51 Northern Sweden NC_000022.10 - 38562924 Jul 13, 2019 (153)
52 Qatari NC_000022.10 - 38562924 Apr 27, 2020 (154)
53 SGDP_PRJ NC_000022.10 - 38562924 Apr 27, 2020 (154)
54 Siberian NC_000022.10 - 38562924 Apr 27, 2020 (154)
55 8.3KJPN NC_000022.10 - 38562924 Apr 27, 2021 (155)
56 TopMed NC_000022.11 - 38166917 Apr 27, 2021 (155)
57 UK 10K study - Twins NC_000022.10 - 38562924 Oct 12, 2018 (152)
58 A Vietnamese Genetic Variation Database NC_000022.10 - 38562924 Jul 13, 2019 (153)
59 ALFA NC_000022.11 - 38166917 Apr 27, 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)
rs59384795 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss117408537, ss208838932, ss283640620, ss287571477, ss1699438013 NC_000022.9:36892869:C:T NC_000022.11:38166916:C:T (self)
80780720, 44684434, 31562802, 5923729, 19910909, 48159105, 17232438, 20976690, 42596695, 11375313, 90667717, 44684434, 9857665, ss228687289, ss238074440, ss244191244, ss566650881, ss662579988, ss995367235, ss1082669844, ss1367226463, ss1429261232, ss1579758790, ss1640026796, ss1683020829, ss1809795962, ss1938934768, ss2030239374, ss2158858959, ss2414424221, ss2704611035, ss2974556926, ss3019329269, ss3352845045, ss3685824554, ss3743947573, ss3759402508, ss3841628398, ss3890579715, ss3940981711, ss5232698410 NC_000022.10:38562923:C:T NC_000022.11:38166916:C:T (self)
570411619, 2258947, 240400860, 384855037, 11209721629, ss2247456825, ss3028956882, ss3377567412, ss3708232379, ss3822564829, ss3847143522, ss5109746090 NC_000022.11:38166916:C:T NC_000022.11:38166916:C:T (self)
ss140787, ss80750543 NT_011520.12:17953492:C:T NC_000022.11:38166916:C:T (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 rs132979

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