GeneBe

chr20-8902709-TA-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000487210.5(PLCB1):​n.*20-59486delA 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 0.00030 ( 0 hom., cov: 0)

Consequence

PLCB1
ENST00000487210.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.691

Publications

1 publications found
Variant links:
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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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
PLCB1ENST00000487210.5 linkn.*20-59486delA intron_variant Intron 24 of 26 1 ENSP00000431704.1 H0YCJ2
PLCB1ENST00000635929.1 linkn.592-59486delA intron_variant Intron 6 of 9 5 ENSP00000490792.1 A0A1B0GW62

Frequencies

GnomAD3 genomes
AF:
0.000303
AC:
44
AN:
145376
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00482
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000450
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000303
AC:
44
AN:
145420
Hom.:
0
Cov.:
0
AF XY:
0.000454
AC XY:
32
AN XY:
70428
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
39450
American (AMR)
AF:
0.00
AC:
0
AN:
14738
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3432
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5012
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4480
European-Finnish (FIN)
AF:
0.00482
AC:
41
AN:
8512
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
284
European-Non Finnish (NFE)
AF:
0.0000450
AC:
3
AN:
66604
Other (OTH)
AF:
0.00
AC:
0
AN:
2010
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.551
Heterozygous variant carriers
0
2
4
6
8
10
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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

Publications

Other links and lift over

dbSNP: rs11087829; hg19: chr20-8883356; API