3-155481290-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014996.4(PLCH1):c.4736G>A(p.Arg1579His) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,614,210 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1579C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014996.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCH1 | ENST00000460012.7 | c.4736G>A | p.Arg1579His | missense_variant | Exon 23 of 23 | 5 | NM_014996.4 | ENSP00000417502.2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251494Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135922
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461882Hom.: 0 Cov.: 33 AF XY: 0.0000454 AC XY: 33AN XY: 727246
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4760G>A (p.R1587H) alteration is located in exon 23 (coding exon 23) of the PLCH1 gene. This alteration results from a G to A substitution at nucleotide position 4760, causing the arginine (R) at amino acid position 1587 to be replaced by a histidine (H). 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