Genetic Variant PLCD1:c.*234delC (chr3-38007538-TG-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006225.4(PLCD1):c.*234delC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 675,396 control chromosomes in the GnomAD database, including 12,919 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 4480 hom., cov: 28)

Exomes 𝑓: 0.16 ( 8439 hom. )

Consequence

PLCD1
NM_006225.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.494

Variant links:

Genes affected

PLCD1 (HGNC:9060): (phospholipase C delta 1) This gene encodes a member of the phospholipase C family. Phospholipase C isozymes play critical roles in intracellular signal transduction by catalyzing the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) into the second messengers diacylglycerol (DAG) and inositol triphosphate (IP3). The encoded protein functions as a tumor suppressor in several types of cancer, and mutations in this gene are a cause of hereditary leukonychia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

PLCD1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 3-38007538-TG-T is Benign according to our data. Variant chr3-38007538-TG-T is described in ClinVar as [Benign]. Clinvar id is 1275453.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PLCD1	NM_006225.4 link	c.*234delC	3_prime_UTR_variant	Exon 15 of 15	ENST00000334661.5	NP_006216.2	P51178-1A8K8F9A0A384MR47
PLCD1	NM_001130964.2 link	c.*234delC	3_prime_UTR_variant	Exon 15 of 15		NP_001124436.1	P51178-2
PLCD1	NR_024071.2 link	n.2732delC	non_coding_transcript_exon_variant	Exon 14 of 14

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PLCD1	ENST00000334661 link	c.*234delC	3_prime_UTR_variant	Exon 15 of 15	1	NM_006225.4	ENSP00000335600.4	P51178-1
PLCD1	ENST00000463876 link	c.*234delC	3_prime_UTR_variant	Exon 15 of 15	2		ENSP00000430344.1	P51178-2
PLCD1	ENST00000417185.6 link	n.642delC	non_coding_transcript_exon_variant	Exon 2 of 2	2
PLCD1	ENST00000461445.5 link	n.3228delC	non_coding_transcript_exon_variant	Exon 12 of 12	2

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32671

AN:

151582

Hom.:

4462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.0858

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.182

GnomAD3 exomes

AF:

0.149

AC:

19537

AN:

130904

Hom.:

2154

AF XY:

0.155

AC XY:

10903

AN XY:

70412

show subpopulations

Gnomad AFR exome

AF:

0.386

Gnomad AMR exome

AF:

0.0733

Gnomad ASJ exome

AF:

0.0876

Gnomad EAS exome

AF:

0.0787

Gnomad SAS exome

AF:

0.240

Gnomad FIN exome

AF:

0.0961

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.136

GnomAD4 exome

AF:

0.160

AC:

83914

AN:

523696

Hom.:

8439

Cov.:

AF XY:

0.165

AC XY:

46318

AN XY:

281268

show subpopulations

Gnomad4 AFR exome

AF:

0.381

Gnomad4 AMR exome

AF:

0.0830

Gnomad4 ASJ exome

AF:

0.0973

Gnomad4 EAS exome

AF:

0.0620

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.117

Gnomad4 NFE exome

AF:

0.158

Gnomad4 OTH exome

AF:

0.163

GnomAD4 genome

AF:

0.216

AC:

32723

AN:

151700

Hom.:

4480

Cov.:

AF XY:

0.212

AC XY:

15705

AN XY:

74138

show subpopulations

Gnomad4 AFR

AF:

0.386

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.109

Gnomad4 EAS

AF:

0.0858

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.164

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.176

Hom.:

560

Bravo

AF:

0.222

Asia WGS

AF:

0.175

AC:

609

AN:

3466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 20, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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