19-48053931-G-A

Variant names:

• chr19-48053931-G-A
• rs891014
• NM_003706.3:c.1430-784C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003706.3(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 NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003706.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4C	NM_003706.3	MANE Select	c.1430-784C>T		intron	N/A	NP_003697.2
	PLA2G4C	NM_001159322.2		c.1460-784C>T		intron	N/A	NP_001152794.1
	PLA2G4C	NM_001159323.2		c.1430-784C>T		intron	N/A	NP_001152795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4C	ENST00000599921.6	TSL:1 MANE Select	c.1430-784C>T		intron	N/A	ENSP00000469473.1
	PLA2G4C	ENST00000594790.1	TSL:1	n.183-784C>T		intron	N/A
	PLA2G4C	ENST00000599111.5	TSL:2	c.1460-784C>T		intron	N/A	ENSP00000472546.1

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

African (AFR) AF: 0.409 AC: 16930 AN: 41428

American (AMR) AF: 0.664 AC: 10107 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2055 AN: 3470

East Asian (EAS) AF: 0.904 AC: 4658 AN: 5154

South Asian (SAS) AF: 0.709 AC: 3412 AN: 4810

European-Finnish (FIN) AF: 0.699 AC: 7364 AN: 10538

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46685 AN: 67940

Other (OTH) AF: 0.634 AC: 1337 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.64
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs891014; hg19: chr19-48557188;