chr20-9372069-C-T

Position:

• chr20-9372069-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001377142.1(PLCB4):​c.586-234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 152,180 control chromosomes in the GnomAD database, including 343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.063 (343 hom., cov: 32)
• Consequence: PLCB4 NM_001377142.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.63

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 20-9372069-C-T is Benign according to our data. Variant chr20-9372069-C-T is described in ClinVar as [Benign]. Clinvar id is 1260941.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLCB4	NM_001377142.1	c.586-234C>T		intron_variant		ENST00000378473.9	NP_001364071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLCB4	ENST00000378473.9	c.586-234C>T		intron_variant		1	NM_001377142.1	ENSP00000367734.5

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9561 AN: 152060 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.0655

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0629 AC: 9572 AN: 152180 Hom.: 343 Cov.: 32 AF XY: 0.0628 AC XY: 4673 AN XY: 74392

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.0511

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0379

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0584

Gnomad4 OTH AF: 0.0648

Alfa AF: 0.0594 Hom.: 29

Bravo AF: 0.0646

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.78

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

Other links and lift over

dbSNP: rs34235974; hg19: chr20-9352716;