Variant 2-218618813-G-A 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_032726.4(PLCD4):c.410+6G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,574,306 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0017 ( 7 hom. )

Consequence

PLCD4
NM_032726.4 splice_donor_region, intron

Scores

Splicing: ADA: 0.0001821

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.654

Variant links:

Genes affected

PLCD4 (HGNC:9062): (phospholipase C delta 4) This gene encodes a member of the delta class of phospholipase C enzymes. Phospholipase C enzymes play a critical role in many cellular processes by hydrolyzing phosphatidylinositol 4,5-bisphosphate into two intracellular second messengers, inositol 1,4,5-trisphosphate and diacylglycerol. Expression of this gene may be a marker for cancer. [provided by RefSeq, Jan 2011]

PLCD4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 2-218618813-G-A is Benign according to our data. Variant chr2-218618813-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651882.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLCD4	NM_032726.4 linkuse as main transcript	c.410+6G>A		splice_donor_region_variant, intron_variant		ENST00000450993.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLCD4	ENST00000450993.7 linkuse as main transcript	c.410+6G>A		splice_donor_region_variant, intron_variant		1	NM_032726.4	P1	Q9BRC7-1

Frequencies

GnomAD3 genomes

AF:

0.00170

AC:

258

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000338

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000851

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00518

Gnomad FIN

AF:

0.00452

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00179

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00245

AC:

454

AN:

185510

Hom.:

AF XY:

0.00264

AC XY:

262

AN XY:

99156

show subpopulations

Gnomad AFR exome

AF:

0.0000945

Gnomad AMR exome

AF:

0.000897

Gnomad ASJ exome

AF:

0.00447

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00513

Gnomad FIN exome

AF:

0.00519

Gnomad NFE exome

AF:

0.00198

Gnomad OTH exome

AF:

0.00281

GnomAD4 exome

AF:

0.00173

AC:

2457

AN:

1422002

Hom.:

Cov.:

AF XY:

0.00188

AC XY:

1326

AN XY:

703622

show subpopulations

Gnomad4 AFR exome

AF:

0.000306

Gnomad4 AMR exome

AF:

0.000918

Gnomad4 ASJ exome

AF:

0.00369

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00460

Gnomad4 FIN exome

AF:

0.00484

Gnomad4 NFE exome

AF:

0.00143

Gnomad4 OTH exome

AF:

0.00190

GnomAD4 genome

AF:

0.00168

AC:

256

AN:

152304

Hom.:

Cov.:

AF XY:

0.00195

AC XY:

145

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.000337

Gnomad4 AMR

AF:

0.000850

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00497

Gnomad4 FIN

AF:

0.00452

Gnomad4 NFE

AF:

0.00179

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00199

Hom.:

Bravo

AF:

0.00114

Asia WGS

AF:

0.00318

AC:

AN:

3478

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

Nov 01, 2022

PLCD4: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.1

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00018

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