chr13-114323879-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032436.4(CHAMP1):c.37C>T(p.Arg13Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,612,102 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. R13H) has been classified as Likely benign.
Frequency
Consequence
NM_032436.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHAMP1 | NM_032436.4 | c.37C>T | p.Arg13Cys | missense_variant | 3/3 | ENST00000361283.4 | |
CHAMP1 | NM_001164144.3 | c.37C>T | p.Arg13Cys | missense_variant | 3/3 | ||
CHAMP1 | NM_001164145.3 | c.37C>T | p.Arg13Cys | missense_variant | 3/3 | ||
CHAMP1 | XM_047430277.1 | c.37C>T | p.Arg13Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHAMP1 | ENST00000361283.4 | c.37C>T | p.Arg13Cys | missense_variant | 3/3 | 1 | NM_032436.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250810Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135558
GnomAD4 exome AF: 0.0000548 AC: 80AN: 1459914Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 39AN XY: 725920
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74346
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | CHAMP1: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at