3-155481050-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014996.4(PLCH1):c.4976A>G(p.Gln1659Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,814 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014996.4 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 |
---|---|---|---|---|---|---|---|
PLCH1 | NM_014996.4 | c.4976A>G | p.Gln1659Arg | missense_variant | 23/23 | ENST00000460012.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCH1 | ENST00000460012.7 | c.4976A>G | p.Gln1659Arg | missense_variant | 23/23 | 5 | NM_014996.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251390Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135876
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461482Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 726944
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.5000A>G (p.Q1667R) alteration is located in exon 23 (coding exon 23) of the PLCH1 gene. This alteration results from a A to G substitution at nucleotide position 5000, causing the glutamine (Q) at amino acid position 1667 to be replaced by an arginine (R). 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