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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.

rs132964

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:38165300 (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=0.120972 (32020/264690, TOPMED)
T=0.115713 (16217/140148, GnomAD)
T=0.09550 (1804/18890, ALFA) (+ 15 more)
T=0.09171 (1537/16760, 8.3KJPN)
T=0.1320 (661/5008, 1000G)
T=0.0527 (236/4480, Estonian)
T=0.0913 (352/3854, 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 (45/322, HapMap)
T=0.125 (27/216, Qatari)
T=0.148 (32/216, 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.38165300C>T
GRCh37.p13 chr 22 NC_000022.10:g.38561307C>T
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.54479G>A
PLA2G6 RefSeqGene NG_007094.2:g.45391G>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+3918…

NM_001004426.3:c.209+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 3 NM_001199562.3:c.209+3918…

NM_001199562.3:c.209+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 4 NM_001349864.2:c.209+3918…

NM_001349864.2:c.209+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 5 NM_001349865.2:c.209+3918…

NM_001349865.2:c.209+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 6 NM_001349866.2:c.209+3918…

NM_001349866.2:c.209+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+391…

NM_001349867.2:c.-457+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+391…

NM_001349868.2:c.-282+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+391…

NM_001349869.2:c.-457+3918G>A

N/A Intron Variant
PLA2G6 transcript variant 1 NM_003560.4:c.209+3918G>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 18890 C=0.90450 T=0.09550
European Sub 14286 C=0.91915 T=0.08085
African Sub 2946 C=0.8337 T=0.1663
African Others Sub 114 C=0.816 T=0.184
African American Sub 2832 C=0.8344 T=0.1656
Asian Sub 112 C=0.857 T=0.143
East Asian Sub 86 C=0.85 T=0.15
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 98 C=0.87 T=0.13
Other Sub 692 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=0.879028 T=0.120972
gnomAD - Genomes Global Study-wide 140148 C=0.884287 T=0.115713
gnomAD - Genomes European Sub 75918 C=0.91367 T=0.08633
gnomAD - Genomes African Sub 41984 C=0.82184 T=0.17816
gnomAD - Genomes American Sub 13644 C=0.91872 T=0.08128
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.8866 T=0.1134
gnomAD - Genomes East Asian Sub 3132 C=0.8550 T=0.1450
gnomAD - Genomes Other Sub 2146 C=0.8868 T=0.1132
8.3KJPN JAPANESE Study-wide 16760 C=0.90829 T=0.09171
1000Genomes Global Study-wide 5008 C=0.8680 T=0.1320
1000Genomes African Sub 1322 C=0.8192 T=0.1808
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=0.860 T=0.140
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=0.9087 T=0.0913
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 322 C=0.860 T=0.140
HapMap American Sub 118 C=0.881 T=0.119
HapMap African Sub 114 C=0.789 T=0.211
HapMap Asian Sub 90 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 216 C=0.852 T=0.148
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.38165300= NC_000022.11:g.38165300C>T
GRCh37.p13 chr 22 NC_000022.10:g.38561307= NC_000022.10:g.38561307C>T
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.54479= NG_007094.3:g.54479G>A
PLA2G6 RefSeqGene NG_007094.2:g.45391= NG_007094.2:g.45391G>A
PLA2G6 transcript variant 2 NM_001004426.1:c.209+3918= NM_001004426.1:c.209+3918G>A
PLA2G6 transcript variant 2 NM_001004426.3:c.209+3918= NM_001004426.3:c.209+3918G>A
PLA2G6 transcript variant 3 NM_001199562.1:c.209+3918= NM_001199562.1:c.209+3918G>A
PLA2G6 transcript variant 3 NM_001199562.3:c.209+3918= NM_001199562.3:c.209+3918G>A
PLA2G6 transcript variant 4 NM_001349864.2:c.209+3918= NM_001349864.2:c.209+3918G>A
PLA2G6 transcript variant 5 NM_001349865.2:c.209+3918= NM_001349865.2:c.209+3918G>A
PLA2G6 transcript variant 6 NM_001349866.2:c.209+3918= NM_001349866.2:c.209+3918G>A
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+3918= NM_001349867.2:c.-457+3918G>A
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+3918= NM_001349868.2:c.-282+3918G>A
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+3918= NM_001349869.2:c.-457+3918G>A
PLA2G6 transcript variant 1 NM_003560.2:c.209+3918= NM_003560.2:c.209+3918G>A
PLA2G6 transcript variant 1 NM_003560.4:c.209+3918= NM_003560.4:c.209+3918G>A
PLA2G6 transcript variant X1 XM_005261764.1:c.209+3918= XM_005261764.1:c.209+3918G>A
PLA2G6 transcript variant X3 XM_005261765.1:c.209+3918= XM_005261765.1:c.209+3918G>A
PLA2G6 transcript variant X2 XM_005261766.1:c.209+3918= XM_005261766.1:c.209+3918G>A
PLA2G6 transcript variant X4 XM_005261767.1:c.209+3918= XM_005261767.1:c.209+3918G>A
PLA2G6 transcript variant X5 XM_005261768.1:c.209+3918= XM_005261768.1:c.209+3918G>A
PLA2G6 transcript variant X6 XM_005261769.1:c.209+3918= XM_005261769.1:c.209+3918G>A
PLA2G6 transcript variant X7 XM_005261770.1:c.-282+3918= XM_005261770.1:c.-282+3918G>A
PLA2G6 transcript variant X8 XM_005261771.1:c.209+3918= XM_005261771.1:c.209+3918G>A
PLA2G6 transcript variant X9 XM_005261772.1:c.209+3918= XM_005261772.1:c.209+3918G>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#.

43 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC ss140772 Jun 24, 2000 (78)
2 KRIBB_YJKIM ss80750537 Dec 15, 2007 (130)
3 1000GENOMES ss112653355 Jan 25, 2009 (130)
4 ILLUMINA-UK ss117408515 Feb 14, 2009 (130)
5 BUSHMAN ss204092328 Jul 04, 2010 (132)
6 BCM-HGSC-SUB ss208842152 Jul 04, 2010 (132)
7 1000GENOMES ss228687275 Jul 14, 2010 (132)
8 1000GENOMES ss238074428 Jul 15, 2010 (132)
9 1000GENOMES ss244191233 Jul 15, 2010 (132)
10 GMI ss283640604 May 04, 2012 (137)
11 GMI ss287571463 Apr 25, 2013 (138)
12 TISHKOFF ss566650859 Apr 25, 2013 (138)
13 SSMP ss662579969 Apr 25, 2013 (138)
14 EVA-GONL ss995367211 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1082669825 Aug 21, 2014 (142)
16 1000GENOMES ss1367226407 Aug 21, 2014 (142)
17 DDI ss1429261215 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1579758774 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1640026760 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1683020793 Apr 01, 2015 (144)
21 EVA_DECODE ss1699437992 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1938934747 Feb 12, 2016 (147)
23 JJLAB ss2030239355 Sep 14, 2016 (149)
24 USC_VALOUEV ss2158858941 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2247456724 Dec 20, 2016 (150)
26 TOPMED ss2414424119 Dec 20, 2016 (150)
27 GRF ss2704611018 Nov 08, 2017 (151)
28 GNOMAD ss2974556805 Nov 08, 2017 (151)
29 SWEGEN ss3019329239 Nov 08, 2017 (151)
30 BIOINF_KMB_FNS_UNIBA ss3028956870 Nov 08, 2017 (151)
31 CSHL ss3352845028 Nov 08, 2017 (151)
32 TOPMED ss3377567139 Nov 08, 2017 (151)
33 EGCUT_WGS ss3685824522 Jul 13, 2019 (153)
34 EVA_DECODE ss3708232346 Jul 13, 2019 (153)
35 ACPOP ss3743947552 Jul 13, 2019 (153)
36 EVA ss3759402484 Jul 13, 2019 (153)
37 KHV_HUMAN_GENOMES ss3822564805 Jul 13, 2019 (153)
38 EVA ss3841628381 Apr 27, 2020 (154)
39 EVA ss3847143505 Apr 27, 2020 (154)
40 SGDP_PRJ ss3890579687 Apr 27, 2020 (154)
41 KRGDB ss3940981676 Apr 27, 2020 (154)
42 TOPMED ss5109745707 Apr 27, 2021 (155)
43 TOMMO_GENOMICS ss5232698350 Apr 27, 2021 (155)
44 1000Genomes NC_000022.10 - 38561307 Oct 12, 2018 (152)
45 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 38561307 Oct 12, 2018 (152)
46 Genetic variation in the Estonian population NC_000022.10 - 38561307 Oct 12, 2018 (152)
47 The Danish reference pan genome NC_000022.10 - 38561307 Apr 27, 2020 (154)
48 gnomAD - Genomes NC_000022.11 - 38165300 Apr 27, 2021 (155)
49 Genome of the Netherlands Release 5 NC_000022.10 - 38561307 Apr 27, 2020 (154)
50 HapMap NC_000022.11 - 38165300 Apr 27, 2020 (154)
51 KOREAN population from KRGDB NC_000022.10 - 38561307 Apr 27, 2020 (154)
52 Northern Sweden NC_000022.10 - 38561307 Jul 13, 2019 (153)
53 Qatari NC_000022.10 - 38561307 Apr 27, 2020 (154)
54 SGDP_PRJ NC_000022.10 - 38561307 Apr 27, 2020 (154)
55 Siberian NC_000022.10 - 38561307 Apr 27, 2020 (154)
56 8.3KJPN NC_000022.10 - 38561307 Apr 27, 2021 (155)
57 TopMed NC_000022.11 - 38165300 Apr 27, 2021 (155)
58 UK 10K study - Twins NC_000022.10 - 38561307 Oct 12, 2018 (152)
59 A Vietnamese Genetic Variation Database NC_000022.10 - 38561307 Jul 13, 2019 (153)
60 ALFA NC_000022.11 - 38165300 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)
rs58262453 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss112653355, ss117408515, ss204092328, ss208842152, ss283640604, ss287571463, ss1699437992 NC_000022.9:36891252:C:T NC_000022.11:38165299:C:T (self)
80780662, 44684397, 31562770, 5923713, 19910885, 48159070, 17232417, 20976669, 42596667, 11375295, 90667657, 44684397, 9857651, ss228687275, ss238074428, ss244191233, ss566650859, ss662579969, ss995367211, ss1082669825, ss1367226407, ss1429261215, ss1579758774, ss1640026760, ss1683020793, ss1938934747, ss2030239355, ss2158858941, ss2414424119, ss2704611018, ss2974556805, ss3019329239, ss3352845028, ss3685824522, ss3743947552, ss3759402484, ss3841628381, ss3890579687, ss3940981676, ss5232698350 NC_000022.10:38561306:C:T NC_000022.11:38165299:C:T (self)
570411311, 2258939, 240400608, 384854654, 2202291802, ss2247456724, ss3028956870, ss3377567139, ss3708232346, ss3822564805, ss3847143505, ss5109745707 NC_000022.11:38165299:C:T NC_000022.11:38165299:C:T (self)
ss140772, ss80750537 NT_011520.12:17951875:C:T NC_000022.11:38165299: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 rs132964

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