Variant chr1-20116338-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_012400.4(PLA2G2D):c.180G>A(p.Thr60=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0099 in 1,614,090 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0072 ( 9 hom., cov: 32)

Exomes 𝑓: 0.010 ( 103 hom. )

Consequence

PLA2G2D
NM_012400.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.69

Variant links:

Genes affected

PLA2G2D (HGNC:9033): (phospholipase A2 group IID) This gene encodes a secreted member of the phospholipase A2 family, and is found in a cluster of related family members on chromosome 1. Phospholipase A2 family members hydrolyze the sn-2 fatty acid ester bond of glycerophospholipids to produce lysophospholipids and free fatty acid. This gene may be involved in inflammation and immune response, and in weight loss associated with chronic obstructive pulmonary disease. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]

PLA2G2D links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 1-20116338-C-T is Benign according to our data. Variant chr1-20116338-C-T is described in ClinVar as [Benign]. Clinvar id is 3250512.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.69 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G2D	NM_012400.4 linkuse as main transcript	c.180G>A	p.Thr60=	synonymous_variant	2/4	ENST00000375105.8
PLA2G2D	NM_001271814.2 linkuse as main transcript	c.180G>A	p.Thr60=	synonymous_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G2D	ENST00000375105.8 linkuse as main transcript	c.180G>A	p.Thr60=	synonymous_variant	2/4	1	NM_012400.4	P1	Q9UNK4-1
PLA2G2D	ENST00000617227.1 linkuse as main transcript	c.180G>A	p.Thr60=	synonymous_variant	2/3	1			Q9UNK4-2

Frequencies

GnomAD3 genomes

AF:

0.00717

AC:

1092

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00198

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.0138

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.00710

AC:

1785

AN:

251316

Hom.:

AF XY:

0.00713

AC XY:

969

AN XY:

135846

show subpopulations

Gnomad AFR exome

AF:

0.00141

Gnomad AMR exome

AF:

0.00182

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.00421

Gnomad FIN exome

AF:

0.0101

Gnomad NFE exome

AF:

0.0112

Gnomad OTH exome

AF:

0.00635

GnomAD4 exome

AF:

0.0102

AC:

14894

AN:

1461772

Hom.:

103

Cov.:

AF XY:

0.00996

AC XY:

7246

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.00140

Gnomad4 AMR exome

AF:

0.00239

Gnomad4 ASJ exome

AF:

0.00390

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.00443

Gnomad4 FIN exome

AF:

0.0100

Gnomad4 NFE exome

AF:

0.0119

Gnomad4 OTH exome

AF:

0.00826

GnomAD4 genome

AF:

0.00717

AC:

1092

AN:

152318

Hom.:

Cov.:

AF XY:

0.00725

AC XY:

540

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00197

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.0138

Gnomad4 NFE

AF:

0.0112

Gnomad4 OTH

AF:

0.00804

Alfa

AF:

0.00920

Hom.:

Bravo

AF:

0.00584

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.0106

EpiControl

AF:

0.0102

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

PLA2G2D: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

0.79

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over