chr20-8902709-T-TA

Variant names:

• chr20-8902709-T-TA
• rs11087829
• ENST00000487210.5:n.*20-59487_*20-59486insA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000487210.5(PLCB1):​n.*20-59487_*20-59486insA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (23345 hom., cov: 0)
• Consequence: PLCB1 ENST00000487210.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCB1	ENST00000487210.5	n.*20-59487_*20-59486insA		intron_variant	Intron 24 of 26	1		ENSP00000431704.1
PLCB1	ENST00000635929.1	n.592-59487_592-59486insA		intron_variant	Intron 6 of 9	5		ENSP00000490792.1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 81412 AN: 145048 Hom.: 23340 Cov.: 0

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.561 AC: 81420 AN: 145092 Hom.: 23345 Cov.: 0 AF XY: 0.555 AC XY: 38985 AN XY: 70266

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11087829; hg19: chr20-8883356;