chr15-40290834-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004573.3(PLCB2):c.3040A>G(p.Ile1014Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCB2 | NM_004573.3 | c.3040A>G | p.Ile1014Val | missense_variant | 28/32 | ENST00000260402.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCB2 | ENST00000260402.8 | c.3040A>G | p.Ile1014Val | missense_variant | 28/32 | 2 | NM_004573.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151614Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248410Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134924
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461034Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 726822
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151614Hom.: 0 Cov.: 30 AF XY: 0.0000405 AC XY: 3AN XY: 74066
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The c.3040A>G (p.I1014V) alteration is located in exon 28 (coding exon 28) of the PLCB2 gene. This alteration results from a A to G substitution at nucleotide position 3040, causing the isoleucine (I) at amino acid position 1014 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