rs8110925

Positions:

• chr19-48060175-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003706.3(PLA2G4C):​c.1257+1823T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,104 control chromosomes in the GnomAD database, including 1,323 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 0.10 (1323 hom., cov: 30)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G4C	NM_003706.3	c.1257+1823T>C		intron_variant		ENST00000599921.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.1257+1823T>C		intron_variant		1	NM_003706.3	A2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15878 AN: 151986 Hom.: 1317 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0307

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.105 AC: 15912 AN: 152104 Hom.: 1323 Cov.: 30 AF XY: 0.101 AC XY: 7507 AN XY: 74374

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0926

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0623

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0739 Hom.: 208

Bravo AF: 0.114

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs8110925; hg19: chr19-48563432;