ENST00000487210.5:n.*20-59487_*20-59486insA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• genetic developmental and epileptic encephalopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• developmental and epileptic encephalopathy, 12

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• infantile spasms

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• malignant migrating partial seizures of infancy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.507 AC: 19943 AN: 39362

American (AMR) AF: 0.473 AC: 6959 AN: 14704

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2454 AN: 3430

East Asian (EAS) AF: 0.356 AC: 1783 AN: 5008

South Asian (SAS) AF: 0.706 AC: 3157 AN: 4474

European-Finnish (FIN) AF: 0.491 AC: 4162 AN: 8478

Middle Eastern (MID) AF: 0.699 AC: 197 AN: 282

European-Non Finnish (NFE) AF: 0.618 AC: 41060 AN: 66456

Other (OTH) AF: 0.591 AC: 1182 AN: 2000

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs11087829; hg19: chr20-8883356;