rs773612198
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_015891.3(CDC40):c.967C>T(p.Arg323Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,613,016 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_015891.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC40 | ENST00000307731.2 | c.967C>T | p.Arg323Cys | missense_variant | Exon 9 of 15 | 1 | NM_015891.3 | ENSP00000304370.1 | ||
CDC40 | ENST00000368932.5 | c.967C>T | p.Arg323Cys | missense_variant | Exon 10 of 16 | 5 | ENSP00000357928.1 | |||
CDC40 | ENST00000368930.5 | c.967C>T | p.Arg323Cys | missense_variant | Exon 9 of 15 | 2 | ENSP00000357926.1 | |||
CDC40 | ENST00000606893.5 | n.2397C>T | non_coding_transcript_exon_variant | Exon 9 of 15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251358Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135850
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461006Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 726884
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.967C>T (p.R323C) alteration is located in exon 9 (coding exon 9) of the CDC40 gene. This alteration results from a C to T substitution at nucleotide position 967, causing the arginine (R) at amino acid position 323 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