chr19-48109583-C-T

Position:

• chr19-48109583-C-T

Variant summary

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

The NM_003706.3(PLA2G4C):​c.-33+904G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,098 control chromosomes in the GnomAD database, including 1,168 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 0.12 (1168 hom., cov: 31)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.-33+904G>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.-33+904G>A		intron_variant		1	NM_003706.3	ENSP00000469473.1

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18387 AN: 151980 Hom.: 1164 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.121 AC: 18408 AN: 152098 Hom.: 1168 Cov.: 31 AF XY: 0.119 AC XY: 8857 AN XY: 74362

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0847

Gnomad4 FIN AF: 0.0877

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.100

Alfa AF: 0.124 Hom.: 208

Bravo AF: 0.124

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.72

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: rs11564509; hg19: chr19-48612840;