3-122359906-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001017928.4(MIX23):c.398G>A(p.Arg133His) variant causes a missense change. The variant allele was found at a frequency of 0.0000401 in 1,569,856 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017928.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIX23 | NM_001017928.4 | c.398G>A | p.Arg133His | missense_variant | Exon 5 of 5 | ENST00000291458.9 | NP_001017928.1 | |
MIX23 | NM_001308326.2 | c.356G>A | p.Arg119His | missense_variant | Exon 5 of 5 | NP_001295255.1 | ||
MIX23 | XM_047447427.1 | c.368G>A | p.Arg123His | missense_variant | Exon 6 of 6 | XP_047303383.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000677 AC: 10AN: 147736Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.0000361 AC: 8AN: 221646Hom.: 0 AF XY: 0.0000495 AC XY: 6AN XY: 121200
GnomAD4 exome AF: 0.0000373 AC: 53AN: 1422120Hom.: 0 Cov.: 34 AF XY: 0.0000467 AC XY: 33AN XY: 707366
GnomAD4 genome AF: 0.0000677 AC: 10AN: 147736Hom.: 1 Cov.: 31 AF XY: 0.0000697 AC XY: 5AN XY: 71742
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.398G>A (p.R133H) alteration is located in exon 5 (coding exon 5) of the CCDC58 gene. This alteration results from a G to A substitution at nucleotide position 398, causing the arginine (R) at amino acid position 133 to be replaced by a histidine (H). 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