20-8595024-C-T

Position:

• chr20-8595024-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015192.4(PLCB1):​c.247-33270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,124 control chromosomes in the GnomAD database, including 1,933 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (1933 hom., cov: 31)
• Consequence: PLCB1 NM_015192.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

PLCB1 (HGNC:15917): (phospholipase C beta 1) 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. This gene is activated by two G-protein alpha subunits, alpha-q and alpha-11. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

PLCB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLCB1	NM_015192.4	c.247-33270C>T		intron_variant		ENST00000338037.11	NP_056007.1
PLCB1	NM_182734.3	c.247-33270C>T		intron_variant			NP_877398.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLCB1	ENST00000338037.11	c.247-33270C>T		intron_variant		1	NM_015192.4	ENSP00000338185.6

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24288 AN: 152006 Hom.: 1925 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.160 AC: 24313 AN: 152124 Hom.: 1933 Cov.: 31 AF XY: 0.156 AC XY: 11627 AN XY: 74376

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.178

Alfa AF: 0.147 Hom.: 939

Bravo AF: 0.158

Asia WGS AF: 0.168 AC: 583 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.52
DANN	Benign	0.83

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: rs6039206; hg19: chr20-8575671;