chr19-48102213-G-A

Variant names:

• chr19-48102213-G-A
• rs8109684
• NM_003706.3:c.258-2353C>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.258-2353C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,804 control chromosomes in the GnomAD database, including 8,103 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 0.31 (8103 hom., cov: 32)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.258-2353C>T		intron_variant	Intron 4 of 16	ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.258-2353C>T		intron_variant	Intron 4 of 16	1	NM_003706.3	ENSP00000469473.1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46575 AN: 151682 Hom.: 8096 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.307 AC: 46590 AN: 151804 Hom.: 8103 Cov.: 32 AF XY: 0.310 AC XY: 22988 AN XY: 74144

African (AFR) AF: 0.145 AC: 6004 AN: 41432

American (AMR) AF: 0.318 AC: 4841 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2665 AN: 5170

South Asian (SAS) AF: 0.327 AC: 1541 AN: 4712

European-Finnish (FIN) AF: 0.396 AC: 4177 AN: 10552

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25332 AN: 67920

Other (OTH) AF: 0.328 AC: 690 AN: 2106

Alfa AF: 0.336 Hom.: 1151

Bravo AF: 0.296

Asia WGS AF: 0.422 AC: 1467 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		-0.94
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: rs8109684; hg19: chr19-48605470;