Genetic Variant PLA2G4C:c.257+1183C>A (chr19-48103405-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003706.3(PLA2G4C):c.257+1183C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,246 control chromosomes in the GnomAD database, including 11,355 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 11347 hom., cov: 31)

Exomes 𝑓: 0.19 ( 8 hom. )

Consequence

PLA2G4C
NM_003706.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.635

Variant links:

Genes affected

PLA2G4C (HGNC:9037): (phospholipase A2 group IVC) This gene encodes a protein which is a member of the phospholipase A2 enzyme family which hydrolyzes glycerophospholipids to produce free fatty acids and lysophospholipids, both of which serve as precursors in the production of signaling molecules. The encoded protein has been shown to be a calcium-independent and membrane bound enzyme. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2009]

PLA2G4C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3 link	c.257+1183C>A		intron_variant	Intron 4 of 16	ENST00000599921.6	NP_003697.2	Q9UP65-1A0A024QZH0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6 link	c.257+1183C>A		intron_variant	Intron 4 of 16	1	NM_003706.3	ENSP00000469473.1		Q9UP65-1

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48442

AN:

151844

Hom.:

11316

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.279

GnomAD4 exome

AF:

0.190

AC:

AN:

284

Hom.:

Cov.:

AF XY:

0.212

AC XY:

AN XY:

212

show subpopulations

Gnomad4 AFR exome

AF:

0.750

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.167

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.143

Gnomad4 NFE exome

AF:

0.178

Gnomad4 OTH exome

AF:

0.227

GnomAD4 genome

AF:

0.319

AC:

48518

AN:

151962

Hom.:

11347

Cov.:

AF XY:

0.315

AC XY:

23374

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.664

Gnomad4 AMR

AF:

0.225

Gnomad4 ASJ

AF:

0.160

Gnomad4 EAS

AF:

0.381

Gnomad4 SAS

AF:

0.218

Gnomad4 FIN

AF:

0.162

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.182

Hom.:

1173

Bravo

AF:

0.341

Asia WGS

AF:

0.317

AC:

1102

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

DANN

Benign

0.45

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over