rs782132271
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032436.4(CHAMP1):c.1417C>T(p.Arg473Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. R473H) has been classified as Likely benign.
Frequency
Consequence
NM_032436.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHAMP1 | NM_032436.4 | c.1417C>T | p.Arg473Cys | missense_variant | 3/3 | ENST00000361283.4 | |
CHAMP1 | NM_001164144.3 | c.1417C>T | p.Arg473Cys | missense_variant | 3/3 | ||
CHAMP1 | NM_001164145.3 | c.1417C>T | p.Arg473Cys | missense_variant | 3/3 | ||
CHAMP1 | XM_047430277.1 | c.1417C>T | p.Arg473Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHAMP1 | ENST00000361283.4 | c.1417C>T | p.Arg473Cys | missense_variant | 3/3 | 1 | NM_032436.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251436Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135894
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727248
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 29, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at