5-138213294-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004661.4(CDC23):āc.19A>Gā(p.Met7Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,386 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M7I) has been classified as Likely benign.
Frequency
Consequence
NM_004661.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC23 | NM_004661.4 | c.19A>G | p.Met7Val | missense_variant | 1/16 | ENST00000394886.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC23 | ENST00000394886.7 | c.19A>G | p.Met7Val | missense_variant | 1/16 | 1 | NM_004661.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000857 AC: 13AN: 151708Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250058Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135546
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461560Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727072
GnomAD4 genome AF: 0.0000856 AC: 13AN: 151826Hom.: 1 Cov.: 32 AF XY: 0.0000944 AC XY: 7AN XY: 74174
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at