Variant chr12-14506992-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_024829.6(PLBD1):c.1313G>A(p.Arg438Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 1,613,944 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0059 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 60 hom. )

Consequence

PLBD1
NM_024829.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.38

Variant links:

Genes affected

PLBD1 (HGNC:26215): (phospholipase B domain containing 1) Predicted to enable phospholipase activity. Predicted to be involved in phospholipid catabolic process. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

PLBD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.01349023).

BP6

Variant 12-14506992-C-T is Benign according to our data. Variant chr12-14506992-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642755.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLBD1	NM_024829.6 linkuse as main transcript	c.1313G>A	p.Arg438Gln	missense_variant	9/11	ENST00000240617.10	NP_079105.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLBD1	ENST00000240617.10 linkuse as main transcript	c.1313G>A	p.Arg438Gln	missense_variant	9/11	1	NM_024829.6	ENSP00000240617	P1

Frequencies

GnomAD3 genomes

AF:

0.00588

AC:

894

AN:

152002

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000942

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00459

Gnomad ASJ

AF:

0.0415

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00737

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00809

Gnomad OTH

AF:

0.00528

GnomAD3 exomes

AF:

0.00612

AC:

1539

AN:

251348

Hom.:

AF XY:

0.00593

AC XY:

806

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00237

Gnomad ASJ exome

AF:

0.0428

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00674

Gnomad NFE exome

AF:

0.00726

Gnomad OTH exome

AF:

0.00587

GnomAD4 exome

AF:

0.00489

AC:

7152

AN:

1461826

Hom.:

Cov.:

AF XY:

0.00490

AC XY:

3567

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.000657

Gnomad4 AMR exome

AF:

0.00248

Gnomad4 ASJ exome

AF:

0.0407

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0000696

Gnomad4 FIN exome

AF:

0.00640

Gnomad4 NFE exome

AF:

0.00471

Gnomad4 OTH exome

AF:

0.00604

GnomAD4 genome

AF:

0.00588

AC:

894

AN:

152118

Hom.:

Cov.:

AF XY:

0.00573

AC XY:

426

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.000939

Gnomad4 AMR

AF:

0.00458

Gnomad4 ASJ

AF:

0.0415

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00737

Gnomad4 NFE

AF:

0.00809

Gnomad4 OTH

AF:

0.00523

Alfa

AF:

0.00819

Hom.:

Bravo

AF:

0.00502

TwinsUK

AF:

0.00243

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00919

AC:

ExAC

AF:

0.00590

AC:

716

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00736

EpiControl

AF:

0.00587

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

PLBD1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.10

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.021

Eigen

Pathogenic

0.84

Eigen_PC

Pathogenic

0.80

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

0.98

M_CAP

Uncertain

0.090

MetaRNN

Benign

0.013

MetaSVM

Benign

-0.91

MutationAssessor

Uncertain

2.8

MutationTaster

Benign

1.0

PrimateAI

Benign

0.46

PROVEAN

Uncertain

-3.7

REVEL

Uncertain

0.53

Sift

Uncertain

0.0040

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.75

MVP

0.55

MPC

0.84

ClinPred

0.040

GERP RS

5.4

Varity_R

0.63

gMVP

0.74

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