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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.

rs142207711

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:136673869 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000091 (24/264690, TOPMED)
A=0.000039 (9/232496, GnomAD_exome)
A=0.000078 (11/140258, GnomAD) (+ 6 more)
A=0.00000 (0/78392, PAGE_STUDY)
A=0.00011 (8/75764, ExAC)
A=0.00006 (2/36066, ALFA)
A=0.00004 (1/28256, 14KJPN)
A=0.00006 (1/16758, 8.3KJPN)
A=0.00008 (1/12976, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
AGPAT2 : Synonymous 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 52266 G=0.99990 A=0.00010
European Sub 36618 G=0.99989 A=0.00011
African Sub 8170 G=0.9999 A=0.0001
African Others Sub 298 G=1.000 A=0.000
African American Sub 7872 G=0.9999 A=0.0001
Asian Sub 146 G=1.000 A=0.000
East Asian Sub 120 G=1.000 A=0.000
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 498 G=1.000 A=0.000
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 6102 G=1.0000 A=0.0000


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 G=0.999909 A=0.000091
gnomAD - Exomes Global Study-wide 232496 G=0.999961 A=0.000039
gnomAD - Exomes European Sub 123924 G=0.999968 A=0.000032
gnomAD - Exomes Asian Sub 46014 G=0.99998 A=0.00002
gnomAD - Exomes American Sub 32672 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 14648 G=0.99973 A=0.00027
gnomAD - Exomes Ashkenazi Jewish Sub 9602 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5636 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140258 G=0.999922 A=0.000078
gnomAD - Genomes European Sub 75944 G=0.99993 A=0.00007
gnomAD - Genomes African Sub 42042 G=0.99986 A=0.00014
gnomAD - Genomes American Sub 13662 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
The PAGE Study Global Study-wide 78392 G=1.00000 A=0.00000
The PAGE Study AfricanAmerican Sub 32306 G=1.00000 A=0.00000
The PAGE Study Mexican Sub 10792 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8288 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7912 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4510 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4224 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3826 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1258 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 844 G=1.000 A=0.000
ExAC Global Study-wide 75764 G=0.99989 A=0.00011
ExAC Europe Sub 45388 G=0.99993 A=0.00007
ExAC Asian Sub 16996 G=0.99994 A=0.00006
ExAC African Sub 6906 G=0.9994 A=0.0006
ExAC American Sub 5978 G=1.0000 A=0.0000
ExAC Other Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 36066 G=0.99994 A=0.00006
Allele Frequency Aggregator European Sub 26648 G=0.99996 A=0.00004
Allele Frequency Aggregator Other Sub 4692 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 3350 G=0.9997 A=0.0003
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 498 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28256 G=0.99996 A=0.00004
8.3KJPN JAPANESE Study-wide 16758 G=0.99994 A=0.00006
GO Exome Sequencing Project Global Study-wide 12976 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8590 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4386 G=0.9998 A=0.0002
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 9 NC_000009.12:g.136673869G>A
GRCh37.p13 chr 9 NC_000009.11:g.139568321G>A
AGPAT2 RefSeqGene NG_008090.1:g.18591C>T
Gene: AGPAT2, 1-acylglycerol-3-phosphate O-acyltransferase 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AGPAT2 transcript variant 1 NM_006412.4:c.720C>T D [GAC] > D [GAT] Coding Sequence Variant
1-acyl-sn-glycerol-3-phosphate acyltransferase beta isoform a NP_006403.2:p.Asp240= D (Asp) > D (Asp) Synonymous Variant
AGPAT2 transcript variant 2 NM_001012727.2:c.624C>T D [GAC] > D [GAT] Coding Sequence Variant
1-acyl-sn-glycerol-3-phosphate acyltransferase beta isoform b NP_001012745.1:p.Asp208= D (Asp) > D (Asp) Synonymous Variant
AGPAT2 transcript variant X1 XM_047422636.1:c.411C>T D [GAC] > D [GAT] Coding Sequence Variant
1-acyl-sn-glycerol-3-phosphate acyltransferase beta isoform X1 XP_047278592.1:p.Asp137= D (Asp) > D (Asp) Synonymous 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.

Allele: A (allele ID: 317517 )
ClinVar Accession Disease Names Clinical Significance
RCV000343775.3 Congenital generalized lipodystrophy type 1 Uncertain-Significance
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 G= A
GRCh38.p14 chr 9 NC_000009.12:g.136673869= NC_000009.12:g.136673869G>A
GRCh37.p13 chr 9 NC_000009.11:g.139568321= NC_000009.11:g.139568321G>A
AGPAT2 RefSeqGene NG_008090.1:g.18591= NG_008090.1:g.18591C>T
AGPAT2 transcript variant 1 NM_006412.4:c.720= NM_006412.4:c.720C>T
AGPAT2 transcript variant 1 NM_006412.3:c.720= NM_006412.3:c.720C>T
AGPAT2 transcript variant 2 NM_001012727.2:c.624= NM_001012727.2:c.624C>T
AGPAT2 transcript variant 2 NM_001012727.1:c.624= NM_001012727.1:c.624C>T
AGPAT2 transcript variant X1 XM_047422636.1:c.411= XM_047422636.1:c.411C>T
1-acyl-sn-glycerol-3-phosphate acyltransferase beta isoform a NP_006403.2:p.Asp240= NP_006403.2:p.Asp240=
1-acyl-sn-glycerol-3-phosphate acyltransferase beta isoform b NP_001012745.1:p.Asp208= NP_001012745.1:p.Asp208=
1-acyl-sn-glycerol-3-phosphate acyltransferase beta isoform X1 XP_047278592.1:p.Asp137= XP_047278592.1:p.Asp137=
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#.

16 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342289471 May 09, 2011 (134)
2 EVA-GONL ss987084682 Aug 21, 2014 (142)
3 EVA_EXAC ss1689755097 Apr 01, 2015 (144)
4 ILLUMINA ss1959228835 Feb 12, 2016 (147)
5 HUMAN_LONGEVITY ss2315269759 Dec 20, 2016 (150)
6 GNOMAD ss2738019897 Nov 08, 2017 (151)
7 GNOMAD ss2748315648 Nov 08, 2017 (151)
8 GNOMAD ss2884350487 Nov 08, 2017 (151)
9 ILLUMINA ss3022978446 Nov 08, 2017 (151)
10 ILLUMINA ss3653535652 Oct 12, 2018 (152)
11 ILLUMINA ss3726654175 Jul 13, 2019 (153)
12 PAGE_CC ss3771534120 Jul 13, 2019 (153)
13 EVA ss3824487601 Apr 26, 2020 (154)
14 TOPMED ss4839074975 Apr 26, 2021 (155)
15 TOMMO_GENOMICS ss5195775283 Apr 26, 2021 (155)
16 TOMMO_GENOMICS ss5740472727 Oct 13, 2022 (156)
17 ExAC NC_000009.11 - 139568321 Oct 12, 2018 (152)
18 gnomAD - Genomes NC_000009.12 - 136673869 Apr 26, 2021 (155)
19 gnomAD - Exomes NC_000009.11 - 139568321 Jul 13, 2019 (153)
20 GO Exome Sequencing Project NC_000009.11 - 139568321 Oct 12, 2018 (152)
21 The PAGE Study NC_000009.12 - 136673869 Jul 13, 2019 (153)
22 8.3KJPN NC_000009.11 - 139568321 Apr 26, 2021 (155)
23 14KJPN NC_000009.12 - 136673869 Oct 13, 2022 (156)
24 TopMed NC_000009.12 - 136673869 Apr 26, 2021 (155)
25 ALFA NC_000009.12 - 136673869 Apr 26, 2021 (155)
26 ClinVar RCV000343775.3 Oct 13, 2022 (156)
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
9897794, 7211131, 945334, 53744590, ss342289471, ss987084682, ss1689755097, ss1959228835, ss2738019897, ss2748315648, ss2884350487, ss3022978446, ss3653535652, ss3824487601, ss5195775283 NC_000009.11:139568320:G:A NC_000009.12:136673868:G:A (self)
RCV000343775.3, 340534894, 755589, 74309831, 676452536, 10861512399, ss2315269759, ss3726654175, ss3771534120, ss4839074975, ss5740472727 NC_000009.12:136673868:G:A NC_000009.12:136673868:G:A (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 rs142207711

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