1-42774827-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_024097.4(C1orf50):c.373C>T(p.Arg125Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024097.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1orf50 | ENST00000372525.7 | c.373C>T | p.Arg125Trp | missense_variant | Exon 4 of 5 | 1 | NM_024097.4 | ENSP00000361603.4 | ||
ENSG00000283580 | ENST00000603943.6 | n.*178C>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 5 | ENSP00000473874.1 | ||||
ENSG00000283580 | ENST00000603943.6 | n.*178C>T | 3_prime_UTR_variant | Exon 3 of 5 | 5 | ENSP00000473874.1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250946Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135660
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461094Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 726888
GnomAD4 genome AF: 0.000138 AC: 21AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.373C>T (p.R125W) alteration is located in exon 4 (coding exon 4) of the C1orf50 gene. This alteration results from a C to T substitution at nucleotide position 373, causing the arginine (R) at amino acid position 125 to be replaced by a tryptophan (W). 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