1-2476647-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014638.4(PLCH2):c.59C>T(p.Ala20Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,607,064 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014638.4 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 |
---|---|---|---|---|---|---|---|
PLCH2 | NM_014638.4 | c.59C>T | p.Ala20Val | missense_variant | 1/22 | ENST00000378486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCH2 | ENST00000378486.8 | c.59C>T | p.Ala20Val | missense_variant | 1/22 | 1 | NM_014638.4 | P2 | |
PLCH2 | ENST00000419816.6 | c.59C>T | p.Ala20Val | missense_variant | 1/22 | 5 | P2 | ||
PLCH2 | ENST00000449969.5 | c.44-1829C>T | intron_variant | 5 | A2 | ||||
PLCH2 | ENST00000609981.5 | c.116-1829C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152192Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000169 AC: 40AN: 236796Hom.: 0 AF XY: 0.000224 AC XY: 29AN XY: 129418
GnomAD4 exome AF: 0.000113 AC: 164AN: 1454872Hom.: 1 Cov.: 31 AF XY: 0.000144 AC XY: 104AN XY: 723406
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152192Hom.: 0 Cov.: 34 AF XY: 0.0000942 AC XY: 7AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.59C>T (p.A20V) alteration is located in exon 1 (coding exon 1) of the PLCH2 gene. This alteration results from a C to T substitution at nucleotide position 59, causing the alanine (A) at amino acid position 20 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