rs2272266

Positions:

• chr3-119618351-C-T

Variant summary

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

The NM_015900.4(PLA1A):​c.922+165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0231 in 152,196 control chromosomes in the GnomAD database, including 116 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 0.023 (116 hom., cov: 32)
• Consequence: PLA1A NM_015900.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

PLA1A (HGNC:17661): (phospholipase A1 member A) The protein encoded by this gene is a phospholipase that hydrolyzes fatty acids at the sn-1 position of phosphatidylserine and 1-acyl-2-lysophosphatidylserine. This secreted protein hydrolyzes phosphatidylserine in liposomes. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

PLA1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA1A	NM_015900.4	c.922+165C>T		intron_variant		ENST00000273371.9	NP_056984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA1A	ENST00000273371.9	c.922+165C>T		intron_variant		1	NM_015900.4	ENSP00000273371.4

Frequencies

GnomAD3 genomes AF: 0.0231 AC: 3518 AN: 152078 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.00394

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0231 AC: 3518 AN: 152196 Hom.: 116 Cov.: 32 AF XY: 0.0254 AC XY: 1888 AN XY: 74426

Gnomad4 AFR AF: 0.00392

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.0219

Gnomad4 OTH AF: 0.0166

Alfa AF: 0.0211 Hom.: 37

Bravo AF: 0.0222

Asia WGS AF: 0.104 AC: 360 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	0.39
DANN	Benign	0.53

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: rs2272266; hg19: chr3-119337198;