19-48066452-G-T

Position:

• chr19-48066452-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003706.3(PLA2G4C):​c.1102+1339C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,730 control chromosomes in the GnomAD database, including 22,735 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 0.54 (22735 hom., cov: 30)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.1102+1339C>A		intron_variant		ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.1102+1339C>A		intron_variant		1	NM_003706.3	ENSP00000469473	A2

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82106 AN: 151610 Hom.: 22714 Cov.: 30

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.529

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.542 AC: 82167 AN: 151730 Hom.: 22735 Cov.: 30 AF XY: 0.535 AC XY: 39674 AN XY: 74124

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.525

Alfa AF: 0.560 Hom.: 31961

Bravo AF: 0.532

Asia WGS AF: 0.331 AC: 1153 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	0.26
DANN	Benign	0.55

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

Other links and lift over

dbSNP: rs1366442; hg19: chr19-48569709;