Variant chr1-20116385-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_012400.4(PLA2G2D):c.133G>A(p.Gly45Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00612 in 1,614,144 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0036 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0064 ( 37 hom. )

Consequence

PLA2G2D
NM_012400.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.55

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 -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.07836455).

BP6

Variant 1-20116385-C-T is Benign according to our data. Variant chr1-20116385-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3257628.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 37 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G2D	NM_012400.4 linkuse as main transcript	c.133G>A	p.Gly45Ser	missense_variant	2/4	ENST00000375105.8	NP_036532.1
PLA2G2D	NM_001271814.2 linkuse as main transcript	c.133G>A	p.Gly45Ser	missense_variant	2/3		NP_001258743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G2D	ENST00000375105.8 linkuse as main transcript	c.133G>A	p.Gly45Ser	missense_variant	2/4	1	NM_012400.4	ENSP00000364246	P1	Q9UNK4-1
PLA2G2D	ENST00000617227.1 linkuse as main transcript	c.133G>A	p.Gly45Ser	missense_variant	2/3	1		ENSP00000482871		Q9UNK4-2

Frequencies

GnomAD3 genomes

AF:

0.00365

AC:

555

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.00691

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00217

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00628

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00402

AC:

1012

AN:

251450

Hom.:

AF XY:

0.00397

AC XY:

540

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00145

Gnomad ASJ exome

AF:

0.00734

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00217

Gnomad NFE exome

AF:

0.00698

Gnomad OTH exome

AF:

0.00407

GnomAD4 exome

AF:

0.00638

AC:

9326

AN:

1461850

Hom.:

Cov.:

AF XY:

0.00612

AC XY:

4450

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.00116

Gnomad4 AMR exome

AF:

0.00159

Gnomad4 ASJ exome

AF:

0.00689

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000104

Gnomad4 FIN exome

AF:

0.00288

Gnomad4 NFE exome

AF:

0.00764

Gnomad4 OTH exome

AF:

0.00596

GnomAD4 genome

AF:

0.00364

AC:

555

AN:

152294

Hom.:

Cov.:

AF XY:

0.00306

AC XY:

228

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.00691

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00217

Gnomad4 NFE

AF:

0.00628

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00594

Hom.:

Bravo

AF:

0.00371

TwinsUK

AF:

0.00701

AC:

ALSPAC

AF:

0.00908

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00674

AC:

ExAC

AF:

0.00442

AC:

537

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00698

EpiControl

AF:

0.00551

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

PLA2G2D: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.76

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Uncertain

0.030

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.30

T;.

Eigen

Pathogenic

0.75

Eigen_PC

Uncertain

0.61

FATHMM_MKL

Uncertain

0.91

LIST_S2

Uncertain

0.89

D;D

M_CAP

Benign

0.056

MetaRNN

Benign

0.078

T;T

MetaSVM

Uncertain

0.29

MutationAssessor

Pathogenic

4.4

H;.

MutationTaster

Benign

0.96

PrimateAI

Benign

0.43

PROVEAN

Pathogenic

-5.9

D;.

REVEL

Uncertain

0.46

Sift

Pathogenic

0.0

D;.

Sift4G

Pathogenic

0.0

D;D

Polyphen

1.0

D;.

Vest4

0.93

MVP

0.84

MPC

0.27

ClinPred

0.13

GERP RS

5.3

Varity_R

0.93

gMVP

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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