Variant 20-9365555-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001377142.1(PLCB4):c.503+41A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 1,242,038 control chromosomes in the GnomAD database, including 3,065 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.050 ( 263 hom., cov: 32)

Exomes 𝑓: 0.067 ( 2802 hom. )

Consequence

PLCB4
NM_001377142.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.252

Variant links:

Genes affected

PLCB4 (HGNC:9059): (phospholipase C beta 4) The protein encoded by this gene catalyzes the formation of inositol 1,4,5-trisphosphate and diacylglycerol from phosphatidylinositol 4,5-bisphosphate. This reaction uses calcium as a cofactor and plays an important role in the intracellular transduction of many extracellular signals in the retina. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2010]

PLCB4 links:

PLCB4 (HGNC:):

PLCB4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 20-9365555-A-G is Benign according to our data. Variant chr20-9365555-A-G is described in ClinVar as [Benign]. Clinvar id is 1288956.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLCB4	NM_001377142.1 linkuse as main transcript	c.503+41A>G		intron_variant		ENST00000378473.9	NP_001364071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLCB4	ENST00000378473.9 linkuse as main transcript	c.503+41A>G		intron_variant		1	NM_001377142.1	ENSP00000367734.5		A0A7P0MRI8

Frequencies

GnomAD3 genomes

AF:

0.0498

AC:

7584

AN:

152138

Hom.:

263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0127

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.0377

Gnomad ASJ

AF:

0.0438

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0501

Gnomad FIN

AF:

0.0676

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0756

Gnomad OTH

AF:

0.0440

GnomAD3 exomes

AF:

0.0537

AC:

12926

AN:

240932

Hom.:

487

AF XY:

0.0558

AC XY:

7258

AN XY:

130102

show subpopulations

Gnomad AFR exome

AF:

0.0112

Gnomad AMR exome

AF:

0.0199

Gnomad ASJ exome

AF:

0.0422

Gnomad EAS exome

AF:

0.000112

Gnomad SAS exome

AF:

0.0555

Gnomad FIN exome

AF:

0.0698

Gnomad NFE exome

AF:

0.0755

Gnomad OTH exome

AF:

0.0550

GnomAD4 exome

AF:

0.0672

AC:

73283

AN:

1089782

Hom.:

2802

Cov.:

AF XY:

0.0673

AC XY:

37606

AN XY:

558670

show subpopulations

Gnomad4 AFR exome

AF:

0.00979

Gnomad4 AMR exome

AF:

0.0213

Gnomad4 ASJ exome

AF:

0.0399

Gnomad4 EAS exome

AF:

0.000106

Gnomad4 SAS exome

AF:

0.0554

Gnomad4 FIN exome

AF:

0.0716

Gnomad4 NFE exome

AF:

0.0774

Gnomad4 OTH exome

AF:

0.0568

GnomAD4 genome

AF:

0.0499

AC:

7591

AN:

152256

Hom.:

263

Cov.:

AF XY:

0.0474

AC XY:

3530

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0127

Gnomad4 AMR

AF:

0.0376

Gnomad4 ASJ

AF:

0.0438

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0508

Gnomad4 FIN

AF:

0.0676

Gnomad4 NFE

AF:

0.0756

Gnomad4 OTH

AF:

0.0450

Alfa

AF:

0.0661

Hom.:

395

Bravo

AF:

0.0454

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.22

DANN

Benign

0.29

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