Variant chr3-193263133-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_020386.5(PLAAT1):c.303G>A(p.Arg101Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00586 in 1,614,108 control chromosomes in the GnomAD database, including 299 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.025 ( 147 hom., cov: 32)

Exomes 𝑓: 0.0038 ( 152 hom. )

Consequence

PLAAT1
NM_020386.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.796

Variant links:

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]

PLAAT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 3-193263133-G-A is Benign according to our data. Variant chr3-193263133-G-A is described in ClinVar as [Benign]. Clinvar id is 786508.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.796 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLAAT1	NM_020386.5 linkuse as main transcript	c.303G>A	p.Arg101Arg	synonymous_variant	3/4	ENST00000264735.4	NP_065119.3	Q9HDD0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PLAAT1	ENST00000264735.4 linkuse as main transcript	c.303G>A	p.Arg101Arg	synonymous_variant	3/4	1	NM_020386.5	ENSP00000264735.4	Q9HDD0-1
PLAAT1	ENST00000650797.1 linkuse as main transcript	c.618G>A	p.Arg206Arg	synonymous_variant	3/4			ENSP00000498228.1	Q9HDD0-2
PLAAT1	ENST00000416012.1 linkuse as main transcript	n.132G>A		non_coding_transcript_exon_variant	1/3	5		ENSP00000414431.1	H7C3Y1

Frequencies

GnomAD3 genomes

AF:

0.0253

AC:

3848

AN:

152126

Hom.:

147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0813

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.0225

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00168

Gnomad OTH

AF:

0.0196

GnomAD3 exomes

AF:

0.00827

AC:

2079

AN:

251444

Hom.:

AF XY:

0.00687

AC XY:

933

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.0859

Gnomad AMR exome

AF:

0.00549

Gnomad ASJ exome

AF:

0.0221

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00137

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00167

Gnomad OTH exome

AF:

0.00619

GnomAD4 exome

AF:

0.00383

AC:

5604

AN:

1461864

Hom.:

152

Cov.:

AF XY:

0.00352

AC XY:

2559

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.0868

Gnomad4 AMR exome

AF:

0.00635

Gnomad4 ASJ exome

AF:

0.0208

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00151

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.00107

Gnomad4 OTH exome

AF:

0.00810

GnomAD4 genome

AF:

0.0253

AC:

3852

AN:

152244

Hom.:

147

Cov.:

AF XY:

0.0251

AC XY:

1868

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0812

Gnomad4 AMR

AF:

0.0143

Gnomad4 ASJ

AF:

0.0225

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00168

Gnomad4 OTH

AF:

0.0194

Alfa

AF:

0.0127

Hom.:

Bravo

AF:

0.0297

Asia WGS

AF:

0.00664

AC:

AN:

3478

EpiCase

AF:

0.00267

EpiControl

AF:

0.00225

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 04, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

0.98

DANN

Benign

0.43

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over