Variant 3-171603117-C-T 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_002662.5(PLD1):c.3186G>A(p.Gly1062=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 1,613,854 control chromosomes in the GnomAD database, including 908 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.047 ( 414 hom., cov: 32)

Exomes 𝑓: 0.015 ( 494 hom. )

Consequence

PLD1
NM_002662.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0930

Variant links:

Genes affected

PLD1 (HGNC:9067): (phospholipase D1) This gene encodes a phosphatidylcholine-specific phospholipase which catalyzes the hydrolysis of phosphatidylcholine in order to yield phosphatidic acid and choline. The enzyme may play a role in signal transduction and subcellular trafficking. Alternative splicing results in multiple transcript variants with both catalytic and regulatory properties. [provided by RefSeq, Sep 2011]

PLD1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 3-171603117-C-T is Benign according to our data. Variant chr3-171603117-C-T is described in ClinVar as [Benign]. Clinvar id is 1266999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.093 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLD1	NM_002662.5 linkuse as main transcript	c.3186G>A	p.Gly1062=	synonymous_variant	27/27	ENST00000351298.9	NP_002653.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLD1	ENST00000351298.9 linkuse as main transcript	c.3186G>A	p.Gly1062=	synonymous_variant	27/27	1	NM_002662.5	ENSP00000342793	A1	Q13393-1
PLD1	ENST00000356327.9 linkuse as main transcript	c.3072G>A	p.Gly1024=	synonymous_variant	26/26	1		ENSP00000348681	P4	Q13393-2

Frequencies

GnomAD3 genomes

AF:

0.0471

AC:

7160

AN:

152070

Hom.:

413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0208

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00396

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.0359

GnomAD3 exomes

AF:

0.0177

AC:

4458

AN:

251216

Hom.:

170

AF XY:

0.0151

AC XY:

2051

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.143

Gnomad AMR exome

AF:

0.0128

Gnomad ASJ exome

AF:

0.00258

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00199

Gnomad FIN exome

AF:

0.00376

Gnomad NFE exome

AF:

0.0129

Gnomad OTH exome

AF:

0.0108

GnomAD4 exome

AF:

0.0152

AC:

22216

AN:

1461666

Hom.:

494

Cov.:

AF XY:

0.0143

AC XY:

10415

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.0144

Gnomad4 ASJ exome

AF:

0.00298

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00218

Gnomad4 FIN exome

AF:

0.00392

Gnomad4 NFE exome

AF:

0.0134

Gnomad4 OTH exome

AF:

0.0196

GnomAD4 genome

AF:

0.0472

AC:

7176

AN:

152188

Hom.:

414

Cov.:

AF XY:

0.0452

AC XY:

3361

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.0207

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00396

Gnomad4 NFE

AF:

0.0133

Gnomad4 OTH

AF:

0.0355

Alfa

AF:

0.0288

Hom.:

101

Bravo

AF:

0.0528

Asia WGS

AF:

0.0130

AC:

AN:

3478

EpiCase

AF:

0.0130

EpiControl

AF:

0.0123

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

5.5

DANN

Benign

0.67

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