6-110213089-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015891.3(CDC40):c.871G>A(p.Val291Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,600,110 control chromosomes in the GnomAD database, including 1 homozygotes. 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC40 | ENST00000307731.2 | c.871G>A | p.Val291Ile | missense_variant | Exon 8 of 15 | 1 | NM_015891.3 | ENSP00000304370.1 | ||
CDC40 | ENST00000368932.5 | c.871G>A | p.Val291Ile | missense_variant | Exon 9 of 16 | 5 | ENSP00000357928.1 | |||
CDC40 | ENST00000368930.5 | c.871G>A | p.Val291Ile | missense_variant | Exon 8 of 15 | 2 | ENSP00000357926.1 | |||
CDC40 | ENST00000606893.5 | n.2301G>A | non_coding_transcript_exon_variant | Exon 8 of 15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251408Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135878
GnomAD4 exome AF: 0.0000780 AC: 113AN: 1447956Hom.: 1 Cov.: 27 AF XY: 0.0000873 AC XY: 63AN XY: 721346
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.871G>A (p.V291I) alteration is located in exon 8 (coding exon 8) of the CDC40 gene. This alteration results from a G to A substitution at nucleotide position 871, causing the valine (V) at amino acid position 291 to be replaced by an isoleucine (I). 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