3-193265909-A-G

Position:

• chr3-193265909-A-G

Variant summary

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

The NM_020386.5(PLAAT1):​c.405+2674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,942 control chromosomes in the GnomAD database, including 14,083 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 0.42 (14083 hom., cov: 32)
• Consequence: PLAAT1 NM_020386.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

PLAAT1 (HGNC:14922): (phospholipase A and acyltransferase 1) Enables acyltransferase activity, transferring groups other than amino-acyl groups and phospholipase activity. Involved in N-acylphosphatidylethanolamine metabolic process and phosphatidylcholine metabolic process. Located in cytoplasm and nucleus. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLAAT1	NM_020386.5	c.405+2674A>G		intron_variant		ENST00000264735.4	NP_065119.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLAAT1	ENST00000264735.4	c.405+2674A>G		intron_variant		1	NM_020386.5	ENSP00000264735.4
PLAAT1	ENST00000650797.1	c.720+2674A>G		intron_variant				ENSP00000498228.1
PLAAT1	ENST00000416012.1	n.234+2674A>G		intron_variant		5		ENSP00000414431.1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63171 AN: 151824 Hom.: 14080 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.416 AC: 63219 AN: 151942 Hom.: 14083 Cov.: 32 AF XY: 0.414 AC XY: 30743 AN XY: 74278

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.437

Alfa AF: 0.375 Hom.: 5584

Bravo AF: 0.431

Asia WGS AF: 0.537 AC: 1865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.70

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: rs3905277; hg19: chr3-192983698;