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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.

rs4376

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:38164738 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.084552 (22380/264690, TOPMED)
C=0.091230 (15191/166514, ALFA)
C=0.081771 (11456/140098, GnomAD) (+ 17 more)
C=0.09200 (1542/16760, 8.3KJPN)
C=0.1010 (506/5008, 1000G)
C=0.0520 (233/4478, Estonian)
C=0.0916 (353/3854, ALSPAC)
C=0.0887 (329/3708, TWINSUK)
C=0.1020 (298/2922, KOREAN)
C=0.0946 (197/2082, HGDP_Stanford)
C=0.1020 (193/1892, HapMap)
C=0.113 (113/998, GoNL)
C=0.095 (57/600, NorthernSweden)
C=0.120 (26/216, Qatari)
C=0.136 (29/214, Vietnamese)
C=0.09 (8/88, Ancient Sardinia)
T=0.47 (40/86, SGDP_PRJ)
C=0.15 (6/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=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.38164738T>C
GRCh37.p13 chr 22 NC_000022.10:g.38560745T>C
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.55041A>G
PLA2G6 RefSeqGene NG_007094.2:g.45953A>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+4480…

NM_001004426.3:c.209+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 3 NM_001199562.3:c.209+4480…

NM_001199562.3:c.209+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 4 NM_001349864.2:c.209+4480…

NM_001349864.2:c.209+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 5 NM_001349865.2:c.209+4480…

NM_001349865.2:c.209+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 6 NM_001349866.2:c.209+4480…

NM_001349866.2:c.209+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+448…

NM_001349867.2:c.-457+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+448…

NM_001349868.2:c.-282+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+448…

NM_001349869.2:c.-457+4480A>G

N/A Intron Variant
PLA2G6 transcript variant 1 NM_003560.4:c.209+4480A>G 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 166514 T=0.908770 C=0.091230
European Sub 145406 T=0.906414 C=0.093586
African Sub 6676 T=0.9302 C=0.0698
African Others Sub 240 T=0.942 C=0.058
African American Sub 6436 T=0.9298 C=0.0702
Asian Sub 674 T=0.887 C=0.113
East Asian Sub 542 T=0.880 C=0.120
Other Asian Sub 132 T=0.917 C=0.083
Latin American 1 Sub 752 T=0.924 C=0.076
Latin American 2 Sub 6330 T=0.9474 C=0.0526
South Asian Sub 184 T=0.870 C=0.130
Other Sub 6492 T=0.9034 C=0.0966


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=0.915448 C=0.084552
gnomAD - Genomes Global Study-wide 140098 T=0.918229 C=0.081771
gnomAD - Genomes European Sub 75876 T=0.91385 C=0.08615
gnomAD - Genomes African Sub 41976 T=0.92975 C=0.07025
gnomAD - Genomes American Sub 13646 T=0.93119 C=0.06881
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.8845 C=0.1155
gnomAD - Genomes East Asian Sub 3128 T=0.8539 C=0.1461
gnomAD - Genomes Other Sub 2148 T=0.9115 C=0.0885
8.3KJPN JAPANESE Study-wide 16760 T=0.90800 C=0.09200
1000Genomes Global Study-wide 5008 T=0.8990 C=0.1010
1000Genomes African Sub 1322 T=0.9334 C=0.0666
1000Genomes East Asian Sub 1008 T=0.8641 C=0.1359
1000Genomes Europe Sub 1006 T=0.9036 C=0.0964
1000Genomes South Asian Sub 978 T=0.860 C=0.140
1000Genomes American Sub 694 T=0.932 C=0.068
Genetic variation in the Estonian population Estonian Study-wide 4478 T=0.9480 C=0.0520
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9084 C=0.0916
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9113 C=0.0887
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.8980 C=0.1020
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 T=0.9054 C=0.0946
HGDP-CEPH-db Supplement 1 Est_Asia Sub 468 T=0.889 C=0.111
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.896 C=0.104
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.869 C=0.131
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.884 C=0.116
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.942 C=0.058
HGDP-CEPH-db Supplement 1 America Sub 216 T=1.000 C=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.93 C=0.07
HapMap Global Study-wide 1892 T=0.8980 C=0.1020
HapMap American Sub 770 T=0.884 C=0.116
HapMap African Sub 692 T=0.916 C=0.084
HapMap Asian Sub 254 T=0.890 C=0.110
HapMap Europe Sub 176 T=0.898 C=0.102
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.887 C=0.113
Northern Sweden ACPOP Study-wide 600 T=0.905 C=0.095
Qatari Global Study-wide 216 T=0.880 C=0.120
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.864 C=0.136
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 88 T=0.91 C=0.09
SGDP_PRJ Global Study-wide 86 T=0.47 C=0.53
The Danish reference pan genome Danish Study-wide 40 T=0.85 C=0.15
Siberian Global Study-wide 4 T=0.5 C=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 T= C
GRCh38.p13 chr 22 NC_000022.11:g.38164738= NC_000022.11:g.38164738T>C
GRCh37.p13 chr 22 NC_000022.10:g.38560745= NC_000022.10:g.38560745T>C
PLA2G6 RefSeqGene (LRG_1015) NG_007094.3:g.55041= NG_007094.3:g.55041A>G
PLA2G6 RefSeqGene NG_007094.2:g.45953= NG_007094.2:g.45953A>G
PLA2G6 transcript variant 2 NM_001004426.1:c.209+4480= NM_001004426.1:c.209+4480A>G
PLA2G6 transcript variant 2 NM_001004426.3:c.209+4480= NM_001004426.3:c.209+4480A>G
PLA2G6 transcript variant 3 NM_001199562.1:c.209+4480= NM_001199562.1:c.209+4480A>G
PLA2G6 transcript variant 3 NM_001199562.3:c.209+4480= NM_001199562.3:c.209+4480A>G
PLA2G6 transcript variant 4 NM_001349864.2:c.209+4480= NM_001349864.2:c.209+4480A>G
PLA2G6 transcript variant 5 NM_001349865.2:c.209+4480= NM_001349865.2:c.209+4480A>G
PLA2G6 transcript variant 6 NM_001349866.2:c.209+4480= NM_001349866.2:c.209+4480A>G
PLA2G6 transcript variant 7 NM_001349867.2:c.-457+4480= NM_001349867.2:c.-457+4480A>G
PLA2G6 transcript variant 8 NM_001349868.2:c.-282+4480= NM_001349868.2:c.-282+4480A>G
PLA2G6 transcript variant 9 NM_001349869.2:c.-457+4480= NM_001349869.2:c.-457+4480A>G
PLA2G6 transcript variant 1 NM_003560.2:c.209+4480= NM_003560.2:c.209+4480A>G
PLA2G6 transcript variant 1 NM_003560.4:c.209+4480= NM_003560.4:c.209+4480A>G
PLA2G6 transcript variant X1 XM_005261764.1:c.209+4480= XM_005261764.1:c.209+4480A>G
PLA2G6 transcript variant X3 XM_005261765.1:c.209+4480= XM_005261765.1:c.209+4480A>G
PLA2G6 transcript variant X2 XM_005261766.1:c.209+4480= XM_005261766.1:c.209+4480A>G
PLA2G6 transcript variant X4 XM_005261767.1:c.209+4480= XM_005261767.1:c.209+4480A>G
PLA2G6 transcript variant X5 XM_005261768.1:c.209+4480= XM_005261768.1:c.209+4480A>G
PLA2G6 transcript variant X6 XM_005261769.1:c.209+4480= XM_005261769.1:c.209+4480A>G
PLA2G6 transcript variant X7 XM_005261770.1:c.-282+4480= XM_005261770.1:c.-282+4480A>G
PLA2G6 transcript variant X8 XM_005261771.1:c.209+4480= XM_005261771.1:c.209+4480A>G
PLA2G6 transcript variant X9 XM_005261772.1:c.209+4480= XM_005261772.1:c.209+4480A>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#.

85 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC ss5137 Sep 19, 2000 (36)
2 KRIBB_YJKIM ss65824235 Nov 29, 2006 (127)
3 ILLUMINA ss67730825 Nov 29, 2006 (127)
4 ILLUMINA ss71380981 May 16, 2007 (127)
5 ILLUMINA ss75340279 Dec 07, 2007 (129)
6 HGSV ss78638392 Dec 07, 2007 (129)
7 KRIBB_YJKIM ss80750508 Dec 14, 2007 (130)
8 1000GENOMES ss112653347 Jan 25, 2009 (130)
9 ILLUMINA-UK ss117408511 Feb 14, 2009 (130)
10 KRIBB_YJKIM ss119337396 Dec 01, 2009 (131)
11 ILLUMINA ss160675820 Dec 01, 2009 (131)
12 ILLUMINA ss173723398 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss208820299 Jul 04, 2010 (132)
14 1000GENOMES ss228687272 Jul 14, 2010 (132)
15 1000GENOMES ss238074426 Jul 15, 2010 (132)
16 1000GENOMES ss244191231 Jul 15, 2010 (132)
17 GMI ss283640602 May 04, 2012 (137)
18 GMI ss287571462 Apr 25, 2013 (138)
19 ILLUMINA ss480934335 May 04, 2012 (137)
20 ILLUMINA ss480953813 May 04, 2012 (137)
21 ILLUMINA ss481917811 Sep 08, 2015 (146)
22 ILLUMINA ss485262145 May 04, 2012 (137)
23 ILLUMINA ss537231494 Sep 08, 2015 (146)
24 TISHKOFF ss566650856 Apr 25, 2013 (138)
25 SSMP ss662579964 Apr 25, 2013 (138)
26 ILLUMINA ss779042656 Aug 21, 2014 (142)
27 ILLUMINA ss783077004 Aug 21, 2014 (142)
28 ILLUMINA ss784034706 Aug 21, 2014 (142)
29 ILLUMINA ss832335247 Apr 01, 2015 (144)
30 ILLUMINA ss834505520 Aug 21, 2014 (142)
31 EVA-GONL ss995367203 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1082669820 Aug 21, 2014 (142)
33 1000GENOMES ss1367226383 Aug 21, 2014 (142)
34 DDI ss1429261214 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1579758772 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1640026751 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1683020784 Apr 01, 2015 (144)
38 EVA_DECODE ss1699437986 Apr 01, 2015 (144)
39 EVA_SVP ss1713742421 Apr 01, 2015 (144)
40 ILLUMINA ss1752421853 Sep 08, 2015 (146)
41 HAMMER_LAB ss1809795944 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1938934744 Feb 12, 2016 (147)
43 JJLAB ss2030239352 Sep 14, 2016 (149)
44 USC_VALOUEV ss2158858938 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2247456694 Dec 20, 2016 (150)
46 TOPMED ss2414424081 Dec 20, 2016 (150)
47 ILLUMINA ss2633880614 Nov 08, 2017 (151)
48 ILLUMINA ss2635112283 Nov 08, 2017 (151)
49 GRF ss2704611015 Nov 08, 2017 (151)
50 ILLUMINA ss2710958463 Nov 08, 2017 (151)
51 GNOMAD ss2974556756 Nov 08, 2017 (151)
52 AFFY ss2985855853 Nov 08, 2017 (151)
53 SWEGEN ss3019329231 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3028956868 Nov 08, 2017 (151)
55 CSHL ss3352845026 Nov 08, 2017 (151)
56 TOPMED ss3377567052 Nov 08, 2017 (151)
57 ILLUMINA ss3628538589 Oct 12, 2018 (152)
58 ILLUMINA ss3631831728 Oct 12, 2018 (152)
59 ILLUMINA ss3633273872 Oct 12, 2018 (152)
60 ILLUMINA ss3633989715 Oct 12, 2018 (152)
61 ILLUMINA ss3634868948 Oct 12, 2018 (152)
62 ILLUMINA ss3635674146 Oct 12, 2018 (152)
63 ILLUMINA ss3636564556 Oct 12, 2018 (152)
64 ILLUMINA ss3637426388 Oct 12, 2018 (152)
65 ILLUMINA ss3638383908 Oct 12, 2018 (152)
66 ILLUMINA ss3640576252 Oct 12, 2018 (152)
67 ILLUMINA ss3641138512 Oct 12, 2018 (152)
68 ILLUMINA ss3641434964 Oct 12, 2018 (152)
69 ILLUMINA ss3643343471 Oct 12, 2018 (152)
70 EGCUT_WGS ss3685824512 Jul 13, 2019 (153)
71 EVA_DECODE ss3708232338 Jul 13, 2019 (153)
72 ACPOP ss3743947547 Jul 13, 2019 (153)
73 ILLUMINA ss3745168796 Jul 13, 2019 (153)
74 EVA ss3759402476 Jul 13, 2019 (153)
75 ILLUMINA ss3772664671 Jul 13, 2019 (153)
76 KHV_HUMAN_GENOMES ss3822564798 Jul 13, 2019 (153)
77 EVA ss3841628378 Apr 27, 2020 (154)
78 EVA ss3847143502 Apr 27, 2020 (154)
79 HGDP ss3847689947 Apr 27, 2020 (154)
80 SGDP_PRJ ss3890579676 Apr 27, 2020 (154)
81 KRGDB ss3940981669 Apr 27, 2020 (154)
82 EVA ss3985918958 Apr 27, 2021 (155)
83 EVA ss4017881739 Apr 27, 2021 (155)
84 TOPMED ss5109745567 Apr 27, 2021 (155)
85 TOMMO_GENOMICS ss5232698334 Apr 27, 2021 (155)
86 1000Genomes NC_000022.10 - 38560745 Oct 12, 2018 (152)
87 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 38560745 Oct 12, 2018 (152)
88 Genetic variation in the Estonian population NC_000022.10 - 38560745 Oct 12, 2018 (152)
89 The Danish reference pan genome NC_000022.10 - 38560745 Apr 27, 2020 (154)
90 gnomAD - Genomes NC_000022.11 - 38164738 Apr 27, 2021 (155)
91 Genome of the Netherlands Release 5 NC_000022.10 - 38560745 Apr 27, 2020 (154)
92 HGDP-CEPH-db Supplement 1 NC_000022.9 - 36890691 Apr 27, 2020 (154)
93 HapMap NC_000022.11 - 38164738 Apr 27, 2020 (154)
94 KOREAN population from KRGDB NC_000022.10 - 38560745 Apr 27, 2020 (154)
95 Northern Sweden NC_000022.10 - 38560745 Jul 13, 2019 (153)
96 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000022.10 - 38560745 Apr 27, 2021 (155)
97 Qatari NC_000022.10 - 38560745 Apr 27, 2020 (154)
98 SGDP_PRJ NC_000022.10 - 38560745 Apr 27, 2020 (154)
99 Siberian NC_000022.10 - 38560745 Apr 27, 2020 (154)
100 8.3KJPN NC_000022.10 - 38560745 Apr 27, 2021 (155)
101 TopMed NC_000022.11 - 38164738 Apr 27, 2021 (155)
102 UK 10K study - Twins NC_000022.10 - 38560745 Oct 12, 2018 (152)
103 A Vietnamese Genetic Variation Database NC_000022.10 - 38560745 Jul 13, 2019 (153)
104 ALFA NC_000022.11 - 38164738 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)
rs58084979 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78638392 NC_000022.8:36885244:T:C NC_000022.11:38164737:T:C (self)
367839, ss112653347, ss117408511, ss160675820, ss208820299, ss283640602, ss287571462, ss480934335, ss1699437986, ss1713742421, ss2635112283, ss3643343471, ss3847689947 NC_000022.9:36890690:T:C NC_000022.11:38164737:T:C (self)
80780637, 44684385, 31562760, 5923711, 19910877, 48159063, 17232412, 1144885, 20976666, 42596656, 11375292, 90667641, 44684385, 9857649, ss228687272, ss238074426, ss244191231, ss480953813, ss481917811, ss485262145, ss537231494, ss566650856, ss662579964, ss779042656, ss783077004, ss784034706, ss832335247, ss834505520, ss995367203, ss1082669820, ss1367226383, ss1429261214, ss1579758772, ss1640026751, ss1683020784, ss1752421853, ss1809795944, ss1938934744, ss2030239352, ss2158858938, ss2414424081, ss2633880614, ss2704611015, ss2710958463, ss2974556756, ss2985855853, ss3019329231, ss3352845026, ss3628538589, ss3631831728, ss3633273872, ss3633989715, ss3634868948, ss3635674146, ss3636564556, ss3637426388, ss3638383908, ss3640576252, ss3641138512, ss3641434964, ss3685824512, ss3743947547, ss3745168796, ss3759402476, ss3772664671, ss3841628378, ss3890579676, ss3940981669, ss3985918958, ss4017881739, ss5232698334 NC_000022.10:38560744:T:C NC_000022.11:38164737:T:C (self)
570411197, 2258937, 240400526, 384854514, 5607570195, ss2247456694, ss3028956868, ss3377567052, ss3708232338, ss3822564798, ss3847143502, ss5109745567 NC_000022.11:38164737:T:C NC_000022.11:38164737:T:C (self)
ss5137, ss65824235, ss67730825, ss71380981, ss75340279, ss80750508, ss119337396, ss173723398 NT_011520.12:17951313:T:C NC_000022.11:38164737: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.

No publications for rs4376

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