rs138077430
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The ENST00000338037.11(PLCB1):c.3643C>A(p.Pro1215Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1215S) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000338037.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLCB1 | NM_015192.4 | c.3643C>A | p.Pro1215Thr | missense_variant | 32/32 | ENST00000338037.11 | NP_056007.1 | |
PLCB1 | NM_182734.3 | c.*239C>A | 3_prime_UTR_variant | 33/33 | NP_877398.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCB1 | ENST00000338037.11 | c.3643C>A | p.Pro1215Thr | missense_variant | 32/32 | 1 | NM_015192.4 | ENSP00000338185 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152156Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456024Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 724692
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at