19-48066452-G-T

Variant names:

• chr19-48066452-G-T
• rs1366442
• NM_003706.3:c.1102+1339C>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.1102+1339C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,730 control chromosomes in the GnomAD database, including 22,735 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 0.54 (22735 hom., cov: 30)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 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.1102+1339C>A		intron	N/A	NP_003697.2
	PLA2G4C	NM_001159322.2		c.1132+1339C>A		intron	N/A	NP_001152794.1
	PLA2G4C	NM_001159323.2		c.1102+1339C>A		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.1102+1339C>A		intron	N/A	ENSP00000469473.1
	PLA2G4C	ENST00000595161.5	TSL:3	c.166+1339C>A		intron	N/A	ENSP00000469528.1
	PLA2G4C	ENST00000599111.5	TSL:2	c.1132+1339C>A		intron	N/A	ENSP00000472546.1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82106 AN: 151610 Hom.: 22714 Cov.: 30

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.542 AC: 82167 AN: 151730 Hom.: 22735 Cov.: 30 AF XY: 0.535 AC XY: 39674 AN XY: 74124

African (AFR) AF: 0.555 AC: 22966 AN: 41356

American (AMR) AF: 0.468 AC: 7115 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.169 AC: 868 AN: 5134

South Asian (SAS) AF: 0.473 AC: 2273 AN: 4806

European-Finnish (FIN) AF: 0.550 AC: 5799 AN: 10540

Middle Eastern (MID) AF: 0.514 AC: 148 AN: 288

European-Non Finnish (NFE) AF: 0.582 AC: 39537 AN: 67914

Other (OTH) AF: 0.525 AC: 1107 AN: 2110

Alfa AF: 0.558 Hom.: 41901

Bravo AF: 0.532

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.55
PhyloP100		-2.3
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: rs1366442; hg19: chr19-48569709;