chr5-55143566-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001170402.1(CDC20B):c.433G>T(p.Ala145Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,610,752 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
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.433G>T | p.Ala145Ser | missense_variant | 4/12 | ENST00000381375.7 | |
CDC20B | NM_152623.2 | c.433G>T | p.Ala145Ser | missense_variant | 4/12 | ||
CDC20B | NM_001145734.2 | c.433G>T | p.Ala145Ser | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20B | ENST00000381375.7 | c.433G>T | p.Ala145Ser | missense_variant | 4/12 | 1 | NM_001170402.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250428Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135412
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1458628Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 2AN XY: 725776
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2022 | The c.433G>T (p.A145S) alteration is located in exon 4 (coding exon 4) of the CDC20B gene. This alteration results from a G to T substitution at nucleotide position 433, causing the alanine (A) at amino acid position 145 to be replaced by a serine (S). 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