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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.

rs84473

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:38161319 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.477143 (126295/264690, TOPMED)
T=0.487317 (68122/139790, GnomAD)
C=0.37852 (6344/16760, 8.3KJPN) (+ 15 more)
C=0.34157 (3678/10768, ALFA)
T=0.4567 (2287/5008, 1000G)
C=0.4109 (1841/4480, Estonian)
C=0.4691 (1808/3854, ALSPAC)
C=0.4698 (1742/3708, TWINSUK)
C=0.3556 (1042/2930, KOREAN)
C=0.3619 (663/1832, Korea1K)
C=0.468 (467/998, GoNL)
C=0.482 (289/600, NorthernSweden)
T=0.303 (122/402, SGDP_PRJ)
T=0.479 (157/328, HapMap)
T=0.426 (92/216, Qatari)
C=0.362 (76/210, Vietnamese)
T=0.47 (19/40, GENOME_DK)
T=0.32 (9/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PLA2G6 : Intron Variant
Publications
1 citation
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.38161319T>A
GRCh38.p13 chr 22 NC_000022.11:g.38161319T>C
GRCh37.p13 chr 22 NC_000022.10:g.38557326T>A
GRCh37.p13 chr 22 NC_000022.10:g.38557326T>C
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.58460A>T
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.58460A>G
PLA2G6 RefSeqGene NG_007094.2:g.49372A>T
PLA2G6 RefSeqGene NG_007094.2:g.49372A>G
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+7899…

NM_001004426.3:c.209+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 3 NM_001199562.3:c.209+7899…

NM_001199562.3:c.209+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 4 NM_001349864.2:c.209+7899…

NM_001349864.2:c.209+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 5 NM_001349865.2:c.209+7899…

NM_001349865.2:c.209+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 6 NM_001349866.2:c.209+7899…

NM_001349866.2:c.209+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+789…

NM_001349867.2:c.-457+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+789…

NM_001349868.2:c.-282+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+789…

NM_001349869.2:c.-457+7899A>T

N/A Intron Variant
PLA2G6 transcript variant 1 NM_003560.4:c.209+7899A>T 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 10768 T=0.65843 A=0.00000, C=0.34157
European Sub 9214 T=0.6547 A=0.0000, C=0.3453
African Sub 1002 T=0.6048 A=0.0000, C=0.3952
African Others Sub 38 T=0.45 A=0.00, C=0.55
African American Sub 964 T=0.611 A=0.000, C=0.389
Asian Sub 42 T=0.98 A=0.00, C=0.02
East Asian Sub 30 T=1.00 A=0.00, C=0.00
Other Asian Sub 12 T=0.92 A=0.00, C=0.08
Latin American 1 Sub 36 T=1.00 A=0.00, C=0.00
Latin American 2 Sub 128 T=1.000 A=0.000, C=0.000
South Asian Sub 12 T=0.83 A=0.00, C=0.17
Other Sub 334 T=0.710 A=0.000, C=0.290


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 T=0.477143 C=0.522857
gnomAD - Genomes Global Study-wide 139790 T=0.487317 C=0.512683
gnomAD - Genomes European Sub 75766 T=0.54226 C=0.45774
gnomAD - Genomes African Sub 41842 T=0.37563 C=0.62437
gnomAD - Genomes American Sub 13600 T=0.48853 C=0.51147
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.5229 C=0.4771
gnomAD - Genomes East Asian Sub 3112 T=0.6038 C=0.3962
gnomAD - Genomes Other Sub 2148 T=0.4935 C=0.5065
8.3KJPN JAPANESE Study-wide 16760 T=0.62148 C=0.37852
1000Genomes Global Study-wide 5008 T=0.4567 C=0.5433
1000Genomes African Sub 1322 T=0.3359 C=0.6641
1000Genomes East Asian Sub 1008 T=0.6230 C=0.3770
1000Genomes Europe Sub 1006 T=0.5318 C=0.4682
1000Genomes South Asian Sub 978 T=0.335 C=0.665
1000Genomes American Sub 694 T=0.507 C=0.493
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5891 C=0.4109
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.5309 C=0.4691
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.5302 C=0.4698
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.6444 C=0.3556
Korean Genome Project KOREAN Study-wide 1832 T=0.6381 C=0.3619
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.532 C=0.468
Northern Sweden ACPOP Study-wide 600 T=0.518 C=0.482
SGDP_PRJ Global Study-wide 402 T=0.303 C=0.697
HapMap Global Study-wide 328 T=0.479 C=0.521
HapMap African Sub 120 T=0.292 C=0.708
HapMap American Sub 120 T=0.492 C=0.508
HapMap Asian Sub 88 T=0.72 C=0.28
Qatari Global Study-wide 216 T=0.426 C=0.574
A Vietnamese Genetic Variation Database Global Study-wide 210 T=0.638 C=0.362
The Danish reference pan genome Danish Study-wide 40 T=0.47 C=0.53
Siberian Global Study-wide 28 T=0.32 C=0.68
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 T= A C
GRCh38.p13 chr 22 NC_000022.11:g.38161319= NC_000022.11:g.38161319T>A NC_000022.11:g.38161319T>C
GRCh37.p13 chr 22 NC_000022.10:g.38557326= NC_000022.10:g.38557326T>A NC_000022.10:g.38557326T>C
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.58460= NG_007094.3:g.58460A>T NG_007094.3:g.58460A>G
PLA2G6 RefSeqGene NG_007094.2:g.49372= NG_007094.2:g.49372A>T NG_007094.2:g.49372A>G
PLA2G6 transcript variant 2 NM_001004426.1:c.209+7899= NM_001004426.1:c.209+7899A>T NM_001004426.1:c.209+7899A>G
PLA2G6 transcript variant 2 NM_001004426.3:c.209+7899= NM_001004426.3:c.209+7899A>T NM_001004426.3:c.209+7899A>G
PLA2G6 transcript variant 3 NM_001199562.1:c.209+7899= NM_001199562.1:c.209+7899A>T NM_001199562.1:c.209+7899A>G
PLA2G6 transcript variant 3 NM_001199562.3:c.209+7899= NM_001199562.3:c.209+7899A>T NM_001199562.3:c.209+7899A>G
PLA2G6 transcript variant 4 NM_001349864.2:c.209+7899= NM_001349864.2:c.209+7899A>T NM_001349864.2:c.209+7899A>G
PLA2G6 transcript variant 5 NM_001349865.2:c.209+7899= NM_001349865.2:c.209+7899A>T NM_001349865.2:c.209+7899A>G
PLA2G6 transcript variant 6 NM_001349866.2:c.209+7899= NM_001349866.2:c.209+7899A>T NM_001349866.2:c.209+7899A>G
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+7899= NM_001349867.2:c.-457+7899A>T NM_001349867.2:c.-457+7899A>G
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+7899= NM_001349868.2:c.-282+7899A>T NM_001349868.2:c.-282+7899A>G
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+7899= NM_001349869.2:c.-457+7899A>T NM_001349869.2:c.-457+7899A>G
PLA2G6 transcript variant 1 NM_003560.2:c.209+7899= NM_003560.2:c.209+7899A>T NM_003560.2:c.209+7899A>G
PLA2G6 transcript variant 1 NM_003560.4:c.209+7899= NM_003560.4:c.209+7899A>T NM_003560.4:c.209+7899A>G
PLA2G6 transcript variant X1 XM_005261764.1:c.209+7899= XM_005261764.1:c.209+7899A>T XM_005261764.1:c.209+7899A>G
PLA2G6 transcript variant X3 XM_005261765.1:c.209+7899= XM_005261765.1:c.209+7899A>T XM_005261765.1:c.209+7899A>G
PLA2G6 transcript variant X2 XM_005261766.1:c.209+7899= XM_005261766.1:c.209+7899A>T XM_005261766.1:c.209+7899A>G
PLA2G6 transcript variant X4 XM_005261767.1:c.209+7899= XM_005261767.1:c.209+7899A>T XM_005261767.1:c.209+7899A>G
PLA2G6 transcript variant X5 XM_005261768.1:c.209+7899= XM_005261768.1:c.209+7899A>T XM_005261768.1:c.209+7899A>G
PLA2G6 transcript variant X6 XM_005261769.1:c.209+7899= XM_005261769.1:c.209+7899A>T XM_005261769.1:c.209+7899A>G
PLA2G6 transcript variant X7 XM_005261770.1:c.-282+7899= XM_005261770.1:c.-282+7899A>T XM_005261770.1:c.-282+7899A>G
PLA2G6 transcript variant X8 XM_005261771.1:c.209+7899= XM_005261771.1:c.209+7899A>T XM_005261771.1:c.209+7899A>G
PLA2G6 transcript variant X9 XM_005261772.1:c.209+7899= XM_005261772.1:c.209+7899A>T XM_005261772.1:c.209+7899A>G
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#.

71 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss90914 Oct 05, 2000 (87)
2 SC ss140770 Jun 24, 2000 (78)
3 SNP500CANCER ss5586839 Mar 31, 2003 (113)
4 SC_SNP ss8296807 Apr 21, 2003 (114)
5 SC_SNP ss13386187 Dec 05, 2003 (119)
6 CSHL-HAPMAP ss16920015 Feb 27, 2004 (120)
7 SSAHASNP ss21853636 Apr 05, 2004 (121)
8 PERLEGEN ss24531924 Sep 20, 2004 (123)
9 ABI ss41506308 Mar 14, 2006 (126)
10 HGSV ss78823986 Dec 07, 2007 (129)
11 KRIBB_YJKIM ss80750526 Dec 14, 2007 (130)
12 HGSV ss86009053 Dec 14, 2007 (130)
13 BCMHGSC_JDW ss91923796 Mar 24, 2008 (129)
14 1000GENOMES ss112653311 Jan 25, 2009 (130)
15 1000GENOMES ss114224072 Jan 25, 2009 (130)
16 ILLUMINA-UK ss117408494 Dec 01, 2009 (131)
17 ENSEMBL ss138356606 Dec 01, 2009 (131)
18 ENSEMBL ss142562125 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167964507 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss169284447 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss171986692 Jul 04, 2010 (132)
22 BUSHMAN ss204092314 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss208830172 Jul 04, 2010 (132)
24 1000GENOMES ss228687258 Jul 14, 2010 (132)
25 1000GENOMES ss238074415 Jul 15, 2010 (132)
26 1000GENOMES ss244191219 Jul 15, 2010 (132)
27 GMI ss283640587 May 04, 2012 (137)
28 GMI ss287571459 Apr 25, 2013 (138)
29 PJP ss292763571 May 09, 2011 (134)
30 TISHKOFF ss566650834 Apr 25, 2013 (138)
31 SSMP ss662579948 Apr 25, 2013 (138)
32 EVA-GONL ss995367179 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1082669793 Aug 21, 2014 (142)
34 1000GENOMES ss1367226283 Aug 21, 2014 (142)
35 DDI ss1429261206 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1579758761 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1640026698 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1683020731 Apr 01, 2015 (144)
39 EVA_DECODE ss1699437959 Apr 01, 2015 (144)
40 HAMMER_LAB ss1809795928 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1938934715 Feb 12, 2016 (147)
42 GENOMED ss1969275492 Jul 19, 2016 (147)
43 JJLAB ss2030239339 Sep 14, 2016 (149)
44 USC_VALOUEV ss2158858917 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2247456452 Dec 20, 2016 (150)
46 TOPMED ss2414423881 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2629616952 Nov 08, 2017 (151)
48 GRF ss2704611000 Nov 08, 2017 (151)
49 ILLUMINA ss2710958461 Nov 08, 2017 (151)
50 GNOMAD ss2974556471 Nov 08, 2017 (151)
51 SWEGEN ss3019329203 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3028956860 Nov 08, 2017 (151)
53 CSHL ss3352845013 Nov 08, 2017 (151)
54 TOPMED ss3377566412 Nov 08, 2017 (151)
55 URBANLAB ss3651182740 Oct 12, 2018 (152)
56 EGCUT_WGS ss3685824473 Jul 13, 2019 (153)
57 EVA_DECODE ss3708232287 Jul 13, 2019 (153)
58 ACPOP ss3743947527 Jul 13, 2019 (153)
59 EVA ss3759402441 Jul 13, 2019 (153)
60 PACBIO ss3788831056 Jul 13, 2019 (153)
61 PACBIO ss3793696031 Jul 13, 2019 (153)
62 PACBIO ss3798582516 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3822564773 Jul 13, 2019 (153)
64 EVA ss3836000007 Apr 27, 2020 (154)
65 EVA ss3841628370 Apr 27, 2020 (154)
66 EVA ss3847143494 Apr 27, 2020 (154)
67 SGDP_PRJ ss3890579620 Apr 27, 2020 (154)
68 KRGDB ss3940981601 Apr 27, 2020 (154)
69 KOGIC ss3983673180 Apr 27, 2020 (154)
70 TOPMED ss5109744665 Apr 27, 2021 (155)
71 TOMMO_GENOMICS ss5232698236 Apr 27, 2021 (155)
72 1000Genomes NC_000022.10 - 38557326 Oct 12, 2018 (152)
73 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 38557326 Oct 12, 2018 (152)
74 Genetic variation in the Estonian population NC_000022.10 - 38557326 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000022.10 - 38557326 Apr 27, 2020 (154)
76 gnomAD - Genomes NC_000022.11 - 38161319 Apr 27, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000022.10 - 38557326 Apr 27, 2020 (154)
78 HapMap NC_000022.11 - 38161319 Apr 27, 2020 (154)
79 KOREAN population from KRGDB NC_000022.10 - 38557326 Apr 27, 2020 (154)
80 Korean Genome Project NC_000022.11 - 38161319 Apr 27, 2020 (154)
81 Northern Sweden NC_000022.10 - 38557326 Jul 13, 2019 (153)
82 Qatari NC_000022.10 - 38557326 Apr 27, 2020 (154)
83 SGDP_PRJ NC_000022.10 - 38557326 Apr 27, 2020 (154)
84 Siberian NC_000022.10 - 38557326 Apr 27, 2020 (154)
85 8.3KJPN NC_000022.10 - 38557326 Apr 27, 2021 (155)
86 TopMed NC_000022.11 - 38161319 Apr 27, 2021 (155)
87 UK 10K study - Twins NC_000022.10 - 38557326 Oct 12, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000022.10 - 38557326 Jul 13, 2019 (153)
89 ALFA NC_000022.11 - 38161319 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)
rs742160 Oct 23, 2000 (87)
rs17294285 Oct 07, 2004 (123)
rs57033778 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
6792816184 NC_000022.11:38161318:T:A NC_000022.11:38161318:T:A
ss78823986, ss86009053 NC_000022.8:36881825:T:C NC_000022.11:38161318:T:C (self)
ss91923796, ss112653311, ss114224072, ss117408494, ss167964507, ss169284447, ss171986692, ss204092314, ss208830172, ss283640587, ss287571459, ss292763571, ss1699437959 NC_000022.9:36887271:T:C NC_000022.11:38161318:T:C (self)
80780537, 44684330, 31562721, 5923700, 19910853, 48158995, 17232392, 20976637, 42596600, 11375271, 90667543, 44684330, 9857643, ss228687258, ss238074415, ss244191219, ss566650834, ss662579948, ss995367179, ss1082669793, ss1367226283, ss1429261206, ss1579758761, ss1640026698, ss1683020731, ss1809795928, ss1938934715, ss1969275492, ss2030239339, ss2158858917, ss2414423881, ss2629616952, ss2704611000, ss2710958461, ss2974556471, ss3019329203, ss3352845013, ss3685824473, ss3743947527, ss3759402441, ss3788831056, ss3793696031, ss3798582516, ss3836000007, ss3841628370, ss3890579620, ss3940981601, ss5232698236 NC_000022.10:38557325:T:C NC_000022.11:38161318:T:C (self)
570410474, 2258933, 40051181, 240399959, 384853612, 6792816184, ss2247456452, ss3028956860, ss3377566412, ss3651182740, ss3708232287, ss3822564773, ss3847143494, ss3983673180, ss5109744665 NC_000022.11:38161318:T:C NC_000022.11:38161318:T:C (self)
ss13386187, ss16920015, ss21853636 NT_011520.9:17866379:T:C NC_000022.11:38161318:T:C (self)
ss90914, ss140770, ss5586839, ss8296807, ss24531924, ss41506308, ss80750526, ss138356606, ss142562125 NT_011520.12:17947894:T:C NC_000022.11:38161318:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs84473
PMID Title Author Year Journal
18676680 Pathway-based evaluation of 380 candidate genes and lung cancer susceptibility suggests the importance of the cell cycle pathway. Hosgood HD 3rd et al. 2008 Carcinogenesis
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