rs891014

Positions:

• chr19-48053931-G-A
• chr19-48053931-G-C
• chr19-48053931-G-T

Variant summary

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

The ENST00000599921.6(PLA2G4C):​c.1430-784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,874 control chromosomes in the GnomAD database, including 30,140 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 0.61 (30140 hom., cov: 30)
• Consequence: PLA2G4C ENST00000599921.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.1430-784C>T		intron_variant		ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.1430-784C>T		intron_variant		1	NM_003706.3	ENSP00000469473	A2

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93336 AN: 151756 Hom.: 30127 Cov.: 30

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.615 AC: 93374 AN: 151874 Hom.: 30140 Cov.: 30 AF XY: 0.617 AC XY: 45835 AN XY: 74238

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.634

Alfa AF: 0.651 Hom.: 4128

Bravo AF: 0.604

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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: rs891014; hg19: chr19-48557188;