19-48109583-C-T

Variant names:

• chr19-48109583-C-T
• rs11564509
• NM_003706.3:c.-33+904G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.-33+904G>A		intron_variant	Intron 1 of 16	ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.-33+904G>A		intron_variant	Intron 1 of 16	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

African (AFR) AF: 0.155 AC: 6418 AN: 41490

American (AMR) AF: 0.111 AC: 1697 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3466

East Asian (EAS) AF: 0.127 AC: 655 AN: 5170

South Asian (SAS) AF: 0.0847 AC: 409 AN: 4828

European-Finnish (FIN) AF: 0.0877 AC: 929 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7781 AN: 67976

Other (OTH) AF: 0.100 AC: 212 AN: 2110

Alfa AF: 0.125 Hom.: 218

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
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11564509; hg19: chr19-48612840;