chr15-40290751-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004573.3(PLCB2):c.3113+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,612,830 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00036 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000077 ( 1 hom. )
Consequence
PLCB2
NM_004573.3 intron
NM_004573.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.84
Genes affected
PLCB2 (HGNC:9055): (phospholipase C beta 2) The protein encoded by this gene is a phosphodiesterase that catalyzes the hydrolysis of phosphatidylinositol 4,5-bisphosphate to the second messengers inositol 1,4,5-trisphosphate (IP3) and diacylglycerol. The encoded protein is activated by G proteins and has been shown to be involved in the type 2 taste receptor signal transduction pathway. In addition, nuclear factor kappa B can regulate the transcription of this gene, whose protein product is also an important regulator of platelet responses. [provided by RefSeq, Jan 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 15-40290751-G-A is Benign according to our data. Variant chr15-40290751-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 778527.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCB2 | NM_004573.3 | c.3113+10C>T | intron_variant | ENST00000260402.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCB2 | ENST00000260402.8 | c.3113+10C>T | intron_variant | 2 | NM_004573.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000355 AC: 54AN: 152064Hom.: 0 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
54
AN:
152064
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000802 AC: 20AN: 249314Hom.: 0 AF XY: 0.0000961 AC XY: 13AN XY: 135298
GnomAD3 exomes
AF:
AC:
20
AN:
249314
Hom.:
AF XY:
AC XY:
13
AN XY:
135298
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000767 AC: 112AN: 1460648Hom.: 1 Cov.: 33 AF XY: 0.0000839 AC XY: 61AN XY: 726704
GnomAD4 exome
AF:
AC:
112
AN:
1460648
Hom.:
Cov.:
33
AF XY:
AC XY:
61
AN XY:
726704
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000361 AC: 55AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.000323 AC XY: 24AN XY: 74400
GnomAD4 genome
?
AF:
AC:
55
AN:
152182
Hom.:
Cov.:
31
AF XY:
AC XY:
24
AN XY:
74400
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 24, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at