rs61929725

Positions:

• chr11-63613986-C-T

Variant summary

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

The NM_001128203.2(PLAAT3):​c.15+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,512,162 control chromosomes in the GnomAD database, including 13,822 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 0.11 (1051 hom., cov: 32)
  • Exomes 𝑓: 0.13 (12771 hom.)
• Consequence: PLAAT3 NM_001128203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

PLAAT3 (HGNC:17825): (phospholipase A and acyltransferase 3) Enables N-acyltransferase activity; phospholipase A1 activity; and phospholipase A2 activity. Involved in N-acylphosphatidylethanolamine metabolic process. Predicted to be located in several cellular components, including lysosome; nuclear envelope; and peroxisome. Predicted to be active in cytoplasm. Biomarker of seminoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLAAT3	NM_001128203.2	c.15+14G>A		intron_variant		ENST00000415826.3	NP_001121675.1
PLAAT3	NM_007069.3	c.15+14G>A		intron_variant			NP_009000.2
PLAAT3	XM_011544741.2	c.60+2601G>A		intron_variant			XP_011543043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLAAT3	ENST00000415826.3	c.15+14G>A		intron_variant		2	NM_001128203.2	ENSP00000389124	P1
PLAAT3	ENST00000323646.9	c.15+14G>A		intron_variant		1		ENSP00000320337	P1
PLAAT3	ENST00000394613.3	n.159+14G>A		intron_variant, non_coding_transcript_variant		1
PLAAT3	ENST00000544269.1	n.297+2601G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16629 AN: 152182 Hom.: 1053 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.138

GnomAD3 exomes AF: 0.113 AC: 27899 AN: 247108 Hom.: 1880 AF XY: 0.117 AC XY: 15740 AN XY: 134020

Gnomad AFR exome AF: 0.0668

Gnomad AMR exome AF: 0.0670

Gnomad ASJ exome AF: 0.173

Gnomad EAS exome AF: 0.00425

Gnomad SAS exome AF: 0.128

Gnomad FIN exome AF: 0.0812

Gnomad NFE exome AF: 0.146

Gnomad OTH exome AF: 0.142

GnomAD4 exome AF: 0.128 AC: 173912 AN: 1359862 Hom.: 12771 Cov.: 22 AF XY: 0.129 AC XY: 88047 AN XY: 681578

Gnomad4 AFR exome AF: 0.0644

Gnomad4 AMR exome AF: 0.0712

Gnomad4 ASJ exome AF: 0.173

Gnomad4 EAS exome AF: 0.00219

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.0856

Gnomad4 NFE exome AF: 0.138

Gnomad4 OTH exome AF: 0.128

GnomAD4 genome AF: 0.109 AC: 16622 AN: 152300 Hom.: 1051 Cov.: 32 AF XY: 0.106 AC XY: 7906 AN XY: 74472

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0788

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.138

Alfa AF: 0.131 Hom.: 234

Bravo AF: 0.109

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.1
DANN	Benign	0.92

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: rs61929725; hg19: chr11-63381458;