chr15-40290782-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004573.3(PLCB2):c.3092C>T(p.Ala1031Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004573.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCB2 | NM_004573.3 | c.3092C>T | p.Ala1031Val | missense_variant | 28/32 | ENST00000260402.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCB2 | ENST00000260402.8 | c.3092C>T | p.Ala1031Val | missense_variant | 28/32 | 2 | NM_004573.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152024Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000963 AC: 24AN: 249250Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135278
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461662Hom.: 0 Cov.: 34 AF XY: 0.0000316 AC XY: 23AN XY: 727134
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152024Hom.: 0 Cov.: 30 AF XY: 0.0000539 AC XY: 4AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.3092C>T (p.A1031V) alteration is located in exon 28 (coding exon 28) of the PLCB2 gene. This alteration results from a C to T substitution at nucleotide position 3092, causing the alanine (A) at amino acid position 1031 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at