13-114324318-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032436.4(CHAMP1):c.476C>T(p.Pro159Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. P159S) has been classified as Uncertain significance.
Frequency
Consequence
NM_032436.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHAMP1 | NM_032436.4 | c.476C>T | p.Pro159Leu | missense_variant | 3/3 | ENST00000361283.4 | |
CHAMP1 | NM_001164144.3 | c.476C>T | p.Pro159Leu | missense_variant | 3/3 | ||
CHAMP1 | NM_001164145.3 | c.476C>T | p.Pro159Leu | missense_variant | 3/3 | ||
CHAMP1 | XM_047430277.1 | c.476C>T | p.Pro159Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHAMP1 | ENST00000361283.4 | c.476C>T | p.Pro159Leu | missense_variant | 3/3 | 1 | NM_032436.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727232
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
CHAMP1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 06, 2023 | The CHAMP1 c.476C>T variant is predicted to result in the amino acid substitution p.Pro159Leu. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at