rs2272266

Variant names:

• chr3-119618351-C-T
• rs2272266
• NM_015900.4:c.922+165C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

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 (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015900.4. 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
	PLA1A	NM_015900.4	MANE Select	c.922+165C>T		intron	N/A	NP_056984.1
	PLA1A	NM_001206960.2		c.874+165C>T		intron	N/A	NP_001193889.1
	PLA1A	NM_001293225.2		c.874+165C>T		intron	N/A	NP_001280154.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA1A	ENST00000273371.9	TSL:1 MANE Select	c.922+165C>T		intron	N/A	ENSP00000273371.4
	PLA1A	ENST00000494440.5	TSL:1	c.874+165C>T		intron	N/A	ENSP00000418793.1
	PLA1A	ENST00000495992.5	TSL:1	c.874+165C>T		intron	N/A	ENSP00000417326.1

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

African (AFR) AF: 0.00392 AC: 163 AN: 41532

American (AMR) AF: 0.0238 AC: 364 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3470

East Asian (EAS) AF: 0.119 AC: 616 AN: 5176

South Asian (SAS) AF: 0.136 AC: 655 AN: 4816

European-Finnish (FIN) AF: 0.0159 AC: 169 AN: 10596

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0219 AC: 1492 AN: 67992

Other (OTH) AF: 0.0166 AC: 35 AN: 2110

Alfa AF: 0.0204 Hom.: 47

Bravo AF: 0.0222

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.39
DANN	Benign	0.53
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism

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: rs2272266; hg19: chr3-119337198;