3-193265909-A-G

Variant names:

• chr3-193265909-A-G
• rs3905277
• NM_020386.5:c.405+2674A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020386.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAAT1	NM_020386.5	MANE Select	c.405+2674A>G		intron	N/A	NP_065119.3	Q9HDD0-1
	PLAAT1	NM_001366112.1		c.405+2674A>G		intron	N/A	NP_001353041.1	Q9HDD0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAAT1	ENST00000264735.4	TSL:1 MANE Select	c.405+2674A>G		intron	N/A	ENSP00000264735.4	Q9HDD0-1
	PLAAT1	ENST00000650797.1		c.720+2674A>G		intron	N/A	ENSP00000498228.1	Q9HDD0-2
	PLAAT1	ENST00000971782.1		c.420+2674A>G		intron	N/A	ENSP00000641841.1

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

African (AFR) AF: 0.562 AC: 23274 AN: 41422

American (AMR) AF: 0.370 AC: 5651 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2837 AN: 5174

South Asian (SAS) AF: 0.492 AC: 2367 AN: 4814

European-Finnish (FIN) AF: 0.285 AC: 3007 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23392 AN: 67922

Other (OTH) AF: 0.437 AC: 922 AN: 2110

Alfa AF: 0.375 Hom.: 6230

Bravo AF: 0.431

Asia WGS AF: 0.537 AC: 1865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3905277;

hg19: chr3-192983698;