chrX-53428408-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001031745.5(RIBC1):c.325C>T(p.Arg109Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,208,990 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. 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. R109H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001031745.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIBC1 | NM_001031745.5 | c.325C>T | p.Arg109Cys | missense_variant | Exon 5 of 8 | ENST00000375327.6 | NP_001026915.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000537 AC: 6AN: 111684Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33880
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182585Hom.: 0 AF XY: 0.0000298 AC XY: 2AN XY: 67055
GnomAD4 exome AF: 0.0000146 AC: 16AN: 1097306Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 9AN XY: 362674
GnomAD4 genome AF: 0.0000537 AC: 6AN: 111684Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33880
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.325C>T (p.R109C) alteration is located in exon 5 (coding exon 3) of the RIBC1 gene. This alteration results from a C to T substitution at nucleotide position 325, causing the arginine (R) at amino acid position 109 to be replaced by a cysteine (C). 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