NM_001013842.3:c.406C>T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001013842.3(C8orf58):c.406C>T(p.Arg136Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000544 in 1,609,720 control chromosomes in the GnomAD database, including 3 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R136H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001013842.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C8orf58 | NM_001013842.3 | c.406C>T | p.Arg136Cys | missense_variant | Exon 2 of 7 | ENST00000289989.10 | NP_001013864.1 | |
C8orf58 | NM_173686.3 | c.406C>T | p.Arg136Cys | missense_variant | Exon 2 of 7 | NP_775957.2 | ||
C8orf58 | NM_001198827.2 | c.406C>T | p.Arg136Cys | missense_variant | Exon 2 of 6 | NP_001185756.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152260Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000832 AC: 202AN: 242780Hom.: 3 AF XY: 0.000891 AC XY: 118AN XY: 132494
GnomAD4 exome AF: 0.000550 AC: 801AN: 1457342Hom.: 3 Cov.: 32 AF XY: 0.000588 AC XY: 426AN XY: 724526
GnomAD4 genome AF: 0.000486 AC: 74AN: 152378Hom.: 0 Cov.: 33 AF XY: 0.000456 AC XY: 34AN XY: 74524
ClinVar
Submissions by phenotype
not provided Benign:1
C8orf58: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at