Variant chr3-119628713-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_015900.4(PLA1A):c.1134A>G(p.Gln378Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00981 in 1,614,028 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0065 ( 3 hom., cov: 32)

Exomes 𝑓: 0.010 ( 94 hom. )

Consequence

PLA1A
NM_015900.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0620

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 Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 3-119628713-A-G is Benign according to our data. Variant chr3-119628713-A-G is described in ClinVar as [Benign]. Clinvar id is 790979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.062 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA1A	NM_015900.4 linkuse as main transcript	c.1134A>G	p.Gln378Gln	synonymous_variant	10/11	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.1134A>G	p.Gln378Gln	synonymous_variant	10/11	1	NM_015900.4	ENSP00000273371.4	Q53H76-1
PLA1A	ENST00000494440.5 linkuse as main transcript	c.1086A>G	p.Gln362Gln	synonymous_variant	10/11	1		ENSP00000418793.1	G5E9W0
PLA1A	ENST00000495992.5 linkuse as main transcript	c.1086A>G	p.Gln362Gln	synonymous_variant	10/11	1		ENSP00000417326.1	Q53H76-3
PLA1A	ENST00000488919.5 linkuse as main transcript	c.615A>G	p.Gln205Gln	synonymous_variant	9/10	2		ENSP00000420625.1	Q53H76-4

Frequencies

GnomAD3 genomes

AF:

0.00646

AC:

983

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00176

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00222

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00584

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0118

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00667

AC:

1676

AN:

251248

Hom.:

AF XY:

0.00658

AC XY:

894

AN XY:

135792

show subpopulations

Gnomad AFR exome

AF:

0.00185

Gnomad AMR exome

AF:

0.00335

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000849

Gnomad FIN exome

AF:

0.00490

Gnomad NFE exome

AF:

0.0118

Gnomad OTH exome

AF:

0.00815

GnomAD4 exome

AF:

0.0102

AC:

14854

AN:

1461706

Hom.:

Cov.:

AF XY:

0.00973

AC XY:

7077

AN XY:

727162

show subpopulations

Gnomad4 AFR exome

AF:

0.00200

Gnomad4 AMR exome

AF:

0.00353

Gnomad4 ASJ exome

AF:

0.000421

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00103

Gnomad4 FIN exome

AF:

0.00592

Gnomad4 NFE exome

AF:

0.0123

Gnomad4 OTH exome

AF:

0.00825

GnomAD4 genome

AF:

0.00645

AC:

983

AN:

152322

Hom.:

Cov.:

AF XY:

0.00559

AC XY:

416

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00176

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00584

Gnomad4 NFE

AF:

0.0118

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00906

Hom.:

Bravo

AF:

0.00599

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00938

EpiControl

AF:

0.00907

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.047

DANN

Benign

0.38

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