3-155481144-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014996.4(PLCH1):c.4882G>T(p.Ala1628Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. A1628T) 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCH1 | ENST00000460012.7 | c.4882G>T | p.Ala1628Ser | missense_variant | Exon 23 of 23 | 5 | NM_014996.4 | ENSP00000417502.2 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251394Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135880
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461862Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 20AN XY: 727226
GnomAD4 genome AF: 0.000204 AC: 31AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4906G>T (p.A1636S) alteration is located in exon 23 (coding exon 23) of the PLCH1 gene. This alteration results from a G to T substitution at nucleotide position 4906, causing the alanine (A) at amino acid position 1636 to be replaced by a serine (S). 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