rs2282479

chr11-63463437-G-C

Variant summary

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

The NM_001146729.2(PLAAT5):c.*66C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 1,224,936 control chromosomes in the GnomAD database, including 1,940 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 0.026 (215 hom., cov: 32)
  • Exomes 𝑓: 0.028 (1725 hom.)
• Consequence: PLAAT5 NM_001146729.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517

Genes affected

PLAAT5 (HGNC:24978): (phospholipase A and acyltransferase 5) Enables N-acyltransferase activity; phospholipase A1 activity; and phospholipase A2 activity. Acts upstream of or within N-acylphosphatidylethanolamine metabolic process. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLAAT5	NM_001146729.2	c.*66C>G		3_prime_UTR_variant	6/6	ENST00000540857.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLAAT5	ENST00000540857.6	c.*66C>G		3_prime_UTR_variant	6/6	1	NM_001146729.2	A2

Frequencies

GnomAD3 genomes AF: 0.0265 AC: 4026 AN: 152158 Hom.: 217 Cov.: 32

Gnomad AFR AF: 0.00941

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0785

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00835

Gnomad OTH AF: 0.0368

GnomAD4 exome AF: 0.0276 AC: 29586 AN: 1072660 Hom.: 1725 Cov.: 14 AF XY: 0.0294 AC XY: 16139 AN XY: 548202

Gnomad4 AFR exome AF: 0.00757

Gnomad4 AMR exome AF: 0.188

Gnomad4 ASJ exome AF: 0.0218

Gnomad4 EAS exome AF: 0.0770

Gnomad4 SAS exome AF: 0.109

Gnomad4 FIN exome AF: 0.0192

Gnomad4 NFE exome AF: 0.00852

Gnomad4 OTH exome AF: 0.0330

GnomAD4 genome AF: 0.0265 AC: 4031 AN: 152276 Hom.: 215 Cov.: 32 AF XY: 0.0297 AC XY: 2213 AN XY: 74450

Gnomad4 AFR AF: 0.00943

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.0785

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.00835

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.0176 Hom.: 18

Bravo AF: 0.0343

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.7
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: rs2282479; hg19: chr11-63230909; COSMIC: COSV57136179; COSMIC: COSV57136179;