Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs148529696

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:42145777 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.001455 (385/264690, TOPMED)
T=0.001544 (388/251262, GnomAD_exome)
T=0.002387 (471/197352, ALFA) (+ 10 more)
T=0.001490 (209/140274, GnomAD)
T=0.001779 (215/120848, ExAC)
T=0.00042 (33/78698, PAGE_STUDY)
T=0.00185 (24/13004, GO-ESP)
T=0.0003 (2/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
T=0.0016 (7/4480, Estonian)
T=0.0042 (16/3854, ALSPAC)
T=0.0024 (9/3708, TWINSUK)
T=0.004 (4/998, GoNL)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PLA2G4F : 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 213716 C=0.997604 T=0.002396
European Sub 178352 C=0.997314 T=0.002686
African Sub 9792 C=0.9996 T=0.0004
African Others Sub 360 C=1.000 T=0.000
African American Sub 9432 C=0.9996 T=0.0004
Asian Sub 6350 C=1.0000 T=0.0000
East Asian Sub 4502 C=1.0000 T=0.0000
Other Asian Sub 1848 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=1.000 T=0.000
Latin American 2 Sub 968 C=0.998 T=0.002
South Asian Sub 280 C=1.000 T=0.000
Other Sub 17178 C=0.99843 T=0.00157


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=0.998545 T=0.001455
gnomAD - Exomes Global Study-wide 251262 C=0.998456 T=0.001544
gnomAD - Exomes European Sub 135240 C=0.997338 T=0.002662
gnomAD - Exomes Asian Sub 49002 C=0.99996 T=0.00004
gnomAD - Exomes American Sub 34578 C=0.99968 T=0.00032
gnomAD - Exomes African Sub 16244 C=0.99957 T=0.00043
gnomAD - Exomes Ashkenazi Jewish Sub 10072 C=0.99980 T=0.00020
gnomAD - Exomes Other Sub 6126 C=0.9990 T=0.0010
Allele Frequency Aggregator Total Global 197352 C=0.997613 T=0.002387
Allele Frequency Aggregator European Sub 168260 C=0.997349 T=0.002651
Allele Frequency Aggregator Other Sub 15744 C=0.99860 T=0.00140
Allele Frequency Aggregator Asian Sub 6350 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 4954 C=0.9998 T=0.0002
Allele Frequency Aggregator Latin American 2 Sub 968 C=0.998 T=0.002
Allele Frequency Aggregator Latin American 1 Sub 796 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 280 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140274 C=0.998510 T=0.001490
gnomAD - Genomes European Sub 75956 C=0.99766 T=0.00234
gnomAD - Genomes African Sub 42046 C=0.99945 T=0.00055
gnomAD - Genomes American Sub 13666 C=0.99956 T=0.00044
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9991 T=0.0009
ExAC Global Study-wide 120848 C=0.998221 T=0.001779
ExAC Europe Sub 72934 C=0.99715 T=0.00285
ExAC Asian Sub 25132 C=0.99996 T=0.00004
ExAC American Sub 11566 C=0.99991 T=0.00009
ExAC African Sub 10312 C=0.99971 T=0.00029
ExAC Other Sub 904 C=0.998 T=0.002
The PAGE Study Global Study-wide 78698 C=0.99958 T=0.00042
The PAGE Study AfricanAmerican Sub 32514 C=0.99951 T=0.00049
The PAGE Study Mexican Sub 10810 C=0.99963 T=0.00037
The PAGE Study Asian Sub 8316 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=0.9978 T=0.0022
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=0.9996 T=0.0004
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=0.9984 T=0.0016
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13004 C=0.99815 T=0.00185
GO Exome Sequencing Project European American Sub 8598 C=0.9972 T=0.0028
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
1000Genomes_30x Global Study-wide 6404 C=0.9997 T=0.0003
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9984 T=0.0016
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9990 T=0.0010
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9984 T=0.0016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9958 T=0.0042
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9976 T=0.0024
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.996 T=0.004
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 15 NC_000015.10:g.42145777C>T
GRCh37.p13 chr 15 NC_000015.9:g.42437975C>T
Gene: PLA2G4F, phospholipase A2 group IVF (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PLA2G4F transcript variant 1 NM_213600.4:c.1661G>A C [TGT] > Y [TAT] Coding Sequence Variant
cytosolic phospholipase A2 zeta NP_998765.3:p.Cys554Tyr C (Cys) > Y (Tyr) Missense Variant
PLA2G4F transcript variant 2 NR_033151.2:n.1675G>A N/A Non Coding Transcript Variant
PLA2G4F transcript variant X1 XR_931785.1:n.1748G>A N/A Non Coding Transcript Variant
PLA2G4F transcript variant X2 XR_931786.1:n. N/A Genic Downstream Transcript 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 C= T
GRCh38.p14 chr 15 NC_000015.10:g.42145777= NC_000015.10:g.42145777C>T
GRCh37.p13 chr 15 NC_000015.9:g.42437975= NC_000015.9:g.42437975C>T
PLA2G4F transcript variant 1 NM_213600.4:c.1661= NM_213600.4:c.1661G>A
PLA2G4F transcript variant 1 NM_213600.3:c.1661= NM_213600.3:c.1661G>A
PLA2G4F transcript variant 2 NR_033151.2:n.1675= NR_033151.2:n.1675G>A
PLA2G4F transcript variant 2 NR_033151.1:n.1680= NR_033151.1:n.1680G>A
PLA2G4F transcript variant X1 XR_931785.1:n.1748= XR_931785.1:n.1748G>A
cytosolic phospholipase A2 zeta NP_998765.3:p.Cys554= NP_998765.3:p.Cys554Tyr
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#.

45 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342400985 May 09, 2011 (134)
2 1000GENOMES ss489047021 May 04, 2012 (137)
3 EXOME_CHIP ss491493150 May 04, 2012 (137)
4 CLINSEQ_SNP ss491698990 May 04, 2012 (137)
5 ILLUMINA ss780707567 Sep 08, 2015 (146)
6 ILLUMINA ss783382234 Sep 08, 2015 (146)
7 EVA-GONL ss991720885 Aug 21, 2014 (142)
8 1000GENOMES ss1353199166 Aug 21, 2014 (142)
9 EVA_UK10K_ALSPAC ss1632859140 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1675853173 Apr 01, 2015 (144)
11 EVA_EXAC ss1691781033 Apr 01, 2015 (144)
12 ILLUMINA ss1752159718 Sep 08, 2015 (146)
13 ILLUMINA ss1917895268 Feb 12, 2016 (147)
14 ILLUMINA ss1946391493 Feb 12, 2016 (147)
15 ILLUMINA ss1959606887 Feb 12, 2016 (147)
16 JJLAB ss2028342833 Sep 14, 2016 (149)
17 HUMAN_LONGEVITY ss2206242519 Dec 20, 2016 (150)
18 GNOMAD ss2741169424 Nov 08, 2017 (151)
19 GNOMAD ss2749282622 Nov 08, 2017 (151)
20 GNOMAD ss2934126327 Nov 08, 2017 (151)
21 AFFY ss2985672114 Nov 08, 2017 (151)
22 SWEGEN ss3013175552 Nov 08, 2017 (151)
23 ILLUMINA ss3021626426 Nov 08, 2017 (151)
24 ILLUMINA ss3627346081 Oct 12, 2018 (152)
25 ILLUMINA ss3634603275 Oct 12, 2018 (152)
26 ILLUMINA ss3640310599 Oct 12, 2018 (152)
27 ILLUMINA ss3644644605 Oct 12, 2018 (152)
28 ILLUMINA ss3652026641 Oct 12, 2018 (152)
29 EGCUT_WGS ss3680320876 Jul 13, 2019 (153)
30 EVA_DECODE ss3697766406 Jul 13, 2019 (153)
31 ILLUMINA ss3725493555 Jul 13, 2019 (153)
32 ILLUMINA ss3744418825 Jul 13, 2019 (153)
33 ILLUMINA ss3744903822 Jul 13, 2019 (153)
34 PAGE_CC ss3771825473 Jul 13, 2019 (153)
35 ILLUMINA ss3772402490 Jul 13, 2019 (153)
36 EVA ss3824909813 Apr 27, 2020 (154)
37 EVA ss3986644510 Apr 27, 2021 (155)
38 TOPMED ss4988990489 Apr 27, 2021 (155)
39 1000G_HIGH_COVERAGE ss5298210726 Oct 16, 2022 (156)
40 EVA ss5418811463 Oct 16, 2022 (156)
41 1000G_HIGH_COVERAGE ss5599494459 Oct 16, 2022 (156)
42 EVA ss5847740127 Oct 16, 2022 (156)
43 EVA ss5875613002 Oct 16, 2022 (156)
44 EVA ss5948776893 Oct 16, 2022 (156)
45 EVA ss5979458833 Oct 16, 2022 (156)
46 1000Genomes NC_000015.9 - 42437975 Oct 12, 2018 (152)
47 1000Genomes_30x NC_000015.10 - 42145777 Oct 16, 2022 (156)
48 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 42437975 Oct 12, 2018 (152)
49 Genetic variation in the Estonian population NC_000015.9 - 42437975 Oct 12, 2018 (152)
50 ExAC NC_000015.9 - 42437975 Oct 12, 2018 (152)
51 gnomAD - Genomes NC_000015.10 - 42145777 Apr 27, 2021 (155)
52 gnomAD - Exomes NC_000015.9 - 42437975 Jul 13, 2019 (153)
53 GO Exome Sequencing Project NC_000015.9 - 42437975 Oct 12, 2018 (152)
54 Genome of the Netherlands Release 5 NC_000015.9 - 42437975 Apr 27, 2020 (154)
55 The PAGE Study NC_000015.10 - 42145777 Jul 13, 2019 (153)
56 TopMed NC_000015.10 - 42145777 Apr 27, 2021 (155)
57 UK 10K study - Twins NC_000015.9 - 42437975 Oct 12, 2018 (152)
58 ALFA NC_000015.10 - 42145777 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491698990 NC_000015.8:40225266:C:T NC_000015.10:42145776:C:T (self)
66261351, 36783957, 26059124, 2150841, 10431941, 1367093, 16431113, 36783957, ss342400985, ss489047021, ss491493150, ss780707567, ss783382234, ss991720885, ss1353199166, ss1632859140, ss1675853173, ss1691781033, ss1752159718, ss1917895268, ss1946391493, ss1959606887, ss2028342833, ss2741169424, ss2749282622, ss2934126327, ss2985672114, ss3013175552, ss3021626426, ss3627346081, ss3634603275, ss3640310599, ss3644644605, ss3652026641, ss3680320876, ss3744418825, ss3744903822, ss3772402490, ss3824909813, ss3986644510, ss5418811463, ss5847740127, ss5948776893, ss5979458833 NC_000015.9:42437974:C:T NC_000015.10:42145776:C:T (self)
87020394, 467083145, 1046942, 204536149, 12758607760, ss2206242519, ss3697766406, ss3725493555, ss3771825473, ss4988990489, ss5298210726, ss5599494459, ss5875613002 NC_000015.10:42145776:C:T NC_000015.10:42145776: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 rs148529696

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