rs1019785

Positions:

• chr19-48077996-C-G
• chr19-48077996-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.845-172G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,200 control chromosomes in the GnomAD database, including 65,051 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 0.92 (65051 hom., cov: 32)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G4C	NM_003706.3	c.845-172G>C		intron_variant		ENST00000599921.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.845-172G>C		intron_variant		1	NM_003706.3	A2

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140030 AN: 152082 Hom.: 65009 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.969

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.921 AC: 140129 AN: 152200 Hom.: 65051 Cov.: 32 AF XY: 0.924 AC XY: 68746 AN XY: 74416

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.969

Gnomad4 OTH AF: 0.933

Alfa AF: 0.945 Hom.: 7957

Bravo AF: 0.911

Asia WGS AF: 0.968 AC: 3366 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	0.83
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1019785; hg19: chr19-48581253;