Variant chr3-171677678-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002662.5(PLD1):c.1884T>C(p.Arg628Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 1,612,886 control chromosomes in the GnomAD database, including 168,178 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 20667 hom., cov: 32)

Exomes 𝑓: 0.45 ( 147511 hom. )

Consequence

PLD1
NM_002662.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.705

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:

PLD1 (HGNC:):

PLD1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 3-171677678-A-G is Benign according to our data. Variant chr3-171677678-A-G is described in ClinVar as [Benign]. Clinvar id is 1276405.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.705 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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.1884T>C	p.Arg628Arg	synonymous_variant	17/27	ENST00000351298.9	NP_002653.1	Q13393-1Q59EA4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PLD1	ENST00000351298.9 linkuse as main transcript	c.1884T>C	p.Arg628Arg	synonymous_variant	17/27	1	NM_002662.5	ENSP00000342793.4	Q13393-1
PLD1	ENST00000356327.9 linkuse as main transcript	c.1770T>C	p.Arg590Arg	synonymous_variant	16/26	1		ENSP00000348681.5	Q13393-2
PLD1	ENST00000471075.1 linkuse as main transcript	n.176T>C		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

77081

AN:

151874

Hom.:

20619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.680

Gnomad AMI

AF:

0.478

Gnomad AMR

AF:

0.456

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.444

Gnomad OTH

AF:

0.445

GnomAD3 exomes

AF:

0.444

AC:

111545

AN:

251108

Hom.:

25721

AF XY:

0.435

AC XY:

58987

AN XY:

135716

show subpopulations

Gnomad AFR exome

AF:

0.685

Gnomad AMR exome

AF:

0.473

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.350

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.542

Gnomad NFE exome

AF:

0.434

Gnomad OTH exome

AF:

0.413

GnomAD4 exome

AF:

0.446

AC:

650829

AN:

1460894

Hom.:

147511

Cov.:

AF XY:

0.441

AC XY:

320364

AN XY:

726828

show subpopulations

Gnomad4 AFR exome

AF:

0.691

Gnomad4 AMR exome

AF:

0.465

Gnomad4 ASJ exome

AF:

0.349

Gnomad4 EAS exome

AF:

0.345

Gnomad4 SAS exome

AF:

0.350

Gnomad4 FIN exome

AF:

0.537

Gnomad4 NFE exome

AF:

0.448

Gnomad4 OTH exome

AF:

0.428

GnomAD4 genome

AF:

0.508

AC:

77183

AN:

151992

Hom.:

20667

Cov.:

AF XY:

0.508

AC XY:

37767

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.680

Gnomad4 AMR

AF:

0.456

Gnomad4 ASJ

AF:

0.338

Gnomad4 EAS

AF:

0.327

Gnomad4 SAS

AF:

0.347

Gnomad4 FIN

AF:

0.553

Gnomad4 NFE

AF:

0.444

Gnomad4 OTH

AF:

0.445

Alfa

AF:

0.442

Hom.:

33494

Bravo

AF:

0.506

Asia WGS

AF:

0.361

AC:

1258

AN:

3478

EpiCase

AF:

0.423

EpiControl

AF:

0.420

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	Jun 27, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

8.1

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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