3-14113041-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001098502.2(CHCHD4):c.275G>A(p.Arg92Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000998 in 1,613,874 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. R92W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001098502.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHCHD4 | NM_001098502.2 | c.275G>A | p.Arg92Gln | missense_variant | Exon 3 of 3 | ENST00000396914.4 | NP_001091972.1 | |
CHCHD4 | NM_144636.3 | c.314G>A | p.Arg105Gln | missense_variant | Exon 4 of 4 | NP_653237.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHCHD4 | ENST00000396914.4 | c.275G>A | p.Arg92Gln | missense_variant | Exon 3 of 3 | 1 | NM_001098502.2 | ENSP00000380122.3 | ||
CHCHD4 | ENST00000295767.9 | c.314G>A | p.Arg105Gln | missense_variant | Exon 4 of 4 | 2 | ENSP00000295767.5 | |||
CHCHD4 | ENST00000420103.1 | n.*103G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 151992Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000723 AC: 18AN: 249012Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134794
GnomAD4 exome AF: 0.0000923 AC: 135AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000811 AC XY: 59AN XY: 727244
GnomAD4 genome AF: 0.000171 AC: 26AN: 151992Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.314G>A (p.R105Q) alteration is located in exon 4 (coding exon 3) of the CHCHD4 gene. This alteration results from a G to A substitution at nucleotide position 314, causing the arginine (R) at amino acid position 105 to be replaced by a glutamine (Q). 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