Variant 3-119625183-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The NM_015900.4(PLA1A):c.1072G>A(p.Glu358Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

PLA1A
NM_015900.4 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.743

Variant links:

Genes affected

PLA1A (HGNC:17661): (phospholipase A1 member A) The protein encoded by this gene is a phospholipase that hydrolyzes fatty acids at the sn-1 position of phosphatidylserine and 1-acyl-2-lysophosphatidylserine. This secreted protein hydrolyzes phosphatidylserine in liposomes. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

PLA1A links:

PLA1A (HGNC:):

PLA1A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.06144601).

BP6

Variant 3-119625183-G-A is Benign according to our data. Variant chr3-119625183-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2681490.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA1A	NM_015900.4 linkuse as main transcript	c.1072G>A	p.Glu358Lys	missense_variant	9/11	ENST00000273371.9	NP_056984.1	Q53H76-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PLA1A	ENST00000273371.9 linkuse as main transcript	c.1072G>A	p.Glu358Lys	missense_variant	9/11	1	NM_015900.4	ENSP00000273371.4	Q53H76-1
PLA1A	ENST00000494440.5 linkuse as main transcript	c.1024G>A	p.Glu342Lys	missense_variant	9/11	1		ENSP00000418793.1	G5E9W0
PLA1A	ENST00000495992.5 linkuse as main transcript	c.1024G>A	p.Glu342Lys	missense_variant	9/11	1		ENSP00000417326.1	Q53H76-3
PLA1A	ENST00000488919.5 linkuse as main transcript	c.553G>A	p.Glu185Lys	missense_variant	8/10	2		ENSP00000420625.1	Q53H76-4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1461492

Hom.:

Cov.:

AF XY:

0.00000275

AC XY:

AN XY:

727076

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.00e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000193

Hom.:

Bravo

AF:

0.00000756

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma

Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.024

BayesDel_noAF

Benign

-0.27

CADD

Benign

9.0

DANN

Benign

0.26

DEOGEN2

Benign

0.017

T;.;.;.

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.092

LIST_S2

Benign

0.77

T;T;T;T

M_CAP

Uncertain

0.14

MetaRNN

Benign

0.061

T;T;T;T

MetaSVM

Benign

-0.43

MutationAssessor

Benign

0.84

L;.;.;.

PrimateAI

Benign

0.28

PROVEAN

Benign

0.10

N;N;N;N

REVEL

Benign

0.26

Sift

Benign

0.93

T;T;T;T

Sift4G

Benign

0.86

T;T;T;T

Polyphen

0.0090

B;.;B;.

Vest4

0.12

MVP

0.53

MPC

0.048

ClinPred

0.012

GERP RS

-1.4

Varity_R

0.037

gMVP

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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