chr5-55114222-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001170402.1(CDC20B):c.1556A>G(p.Tyr519Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001170402.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC20B | NM_001170402.1 | c.1556A>G | p.Tyr519Cys | missense_variant | 12/12 | ENST00000381375.7 | |
CDC20B | NM_152623.2 | c.1544A>G | p.Tyr515Cys | missense_variant | 12/12 | ||
CDC20B | NM_001145734.2 | c.1430A>G | p.Tyr477Cys | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20B | ENST00000381375.7 | c.1556A>G | p.Tyr519Cys | missense_variant | 12/12 | 1 | NM_001170402.1 | A1 | |
CDC20B | ENST00000296733.5 | c.1544A>G | p.Tyr515Cys | missense_variant | 12/12 | 1 | P4 | ||
CDC20B | ENST00000322374.10 | c.1430A>G | p.Tyr477Cys | missense_variant | 11/11 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461182Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 726892
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.