Genetic Variant NM_001146729.2:c.247G>C (chr11-63488969-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001146729.2(PLAAT5):c.247G>C(p.Ala83Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 1,606,038 control chromosomes in the GnomAD database, including 14,134 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 6492 hom., cov: 32)

Exomes 𝑓: 0.060 ( 7642 hom. )

Consequence

PLAAT5
NM_001146729.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.432

Variant links:

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]

PLAAT5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.247038E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLAAT5	NM_001146729.2 link	c.247G>C	p.Ala83Pro	missense_variant	Exon 3 of 6	ENST00000540857.6	NP_001140201.2	Q8NE88

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLAAT5	ENST00000540857.6 link	c.247G>C	p.Ala83Pro	missense_variant	Exon 3 of 6	1	NM_001146729.2	ENSP00000444809.1		Q96KN8-3

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28889

AN:

151852

Hom.:

6462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.545

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.0921

Gnomad ASJ

AF:

0.0652

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.0360

Gnomad FIN

AF:

0.0525

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0423

Gnomad OTH

AF:

0.143

GnomAD3 exomes

AF:

0.0860

AC:

21511

AN:

250200

Hom.:

3009

AF XY:

0.0747

AC XY:

10104

AN XY:

135280

show subpopulations

Gnomad AFR exome

AF:

0.556

Gnomad AMR exome

AF:

0.0471

Gnomad ASJ exome

AF:

0.0662

Gnomad EAS exome

AF:

0.162

Gnomad SAS exome

AF:

0.0349

Gnomad FIN exome

AF:

0.0472

Gnomad NFE exome

AF:

0.0421

Gnomad OTH exome

AF:

0.0653

GnomAD4 exome

AF:

0.0595

AC:

86562

AN:

1454068

Hom.:

7642

Cov.:

AF XY:

0.0568

AC XY:

41127

AN XY:

723830

show subpopulations

Gnomad4 AFR exome

AF:

0.570

Gnomad4 AMR exome

AF:

0.0523

Gnomad4 ASJ exome

AF:

0.0620

Gnomad4 EAS exome

AF:

0.166

Gnomad4 SAS exome

AF:

0.0331

Gnomad4 FIN exome

AF:

0.0462

Gnomad4 NFE exome

AF:

0.0422

Gnomad4 OTH exome

AF:

0.0819

GnomAD4 genome

AF:

0.191

AC:

28964

AN:

151970

Hom.:

6492

Cov.:

AF XY:

0.186

AC XY:

13832

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.546

Gnomad4 AMR

AF:

0.0919

Gnomad4 ASJ

AF:

0.0652

Gnomad4 EAS

AF:

0.157

Gnomad4 SAS

AF:

0.0354

Gnomad4 FIN

AF:

0.0525

Gnomad4 NFE

AF:

0.0423

Gnomad4 OTH

AF:

0.141

Alfa

AF:

0.0669

Hom.:

860

Bravo

AF:

0.210

TwinsUK

AF:

0.0426

AC:

158

ALSPAC

AF:

0.0426

AC:

164

ESP6500AA

AF:

0.525

AC:

2309

ESP6500EA

AF:

0.0468

AC:

402

ExAC

AF:

0.0944

AC:

11466

Asia WGS

AF:

0.103

AC:

358

AN:

3478

EpiCase

AF:

0.0416

EpiControl

AF:

0.0423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.055

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.24

DANN

Benign

0.099

DEOGEN2

Benign

0.0012

.;.;T

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.0030

LIST_S2

Benign

0.17

T;T;T

MetaRNN

Benign

0.000012

T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

-0.90

.;N;N

PrimateAI

Benign

0.30

PROVEAN

Benign

0.85

N;N;N

REVEL

Benign

0.047

Sift

Benign

1.0

T;T;T

Sift4G

Benign

1.0

T;T;T

Polyphen

0.0

.;.;B

Vest4

0.073

MPC

0.16

ClinPred

0.00026

GERP RS

-1.0

Varity_R

0.063

gMVP

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over