19-48048700-A-T

Variant names:

• chr19-48048700-A-T
• rs1549637
• NM_003706.3:c.1581-312T>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.1581-312T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,122 control chromosomes in the GnomAD database, including 43,964 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 0.73 (43964 hom., cov: 32)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.1581-312T>A		intron_variant	Intron 16 of 16	ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.1581-312T>A		intron_variant	Intron 16 of 16	1	NM_003706.3	ENSP00000469473.1
PLA2G4C	ENST00000594790.1	n.334-312T>A		intron_variant	Intron 2 of 2	1
PLA2G4C	ENST00000599111.5	c.1611-312T>A		intron_variant	Intron 16 of 16	2		ENSP00000472546.1
PLA2G4C	ENST00000354276.7	c.*40-312T>A		intron_variant	Intron 16 of 16	2		ENSP00000346228.2

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111412 AN: 152004 Hom.: 43963 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.733 AC: 111430 AN: 152122 Hom.: 43964 Cov.: 32 AF XY: 0.738 AC XY: 54843 AN XY: 74358

African (AFR) AF: 0.407 AC: 16869 AN: 41466

American (AMR) AF: 0.842 AC: 12871 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2786 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4366 AN: 5174

South Asian (SAS) AF: 0.835 AC: 4025 AN: 4818

European-Finnish (FIN) AF: 0.872 AC: 9240 AN: 10600

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58580 AN: 68002

Other (OTH) AF: 0.782 AC: 1643 AN: 2102

Alfa AF: 0.783 Hom.: 6036

Bravo AF: 0.717

Asia WGS AF: 0.838 AC: 2914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		-0.29
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: rs1549637; hg19: chr19-48551957;