5-55133466-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001170402.1(CDC20B):āc.643T>Cā(p.Ser215Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,585,296 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001170402.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC20B | NM_001170402.1 | c.643T>C | p.Ser215Pro | missense_variant | 6/12 | ENST00000381375.7 | |
CDC20B | NM_152623.2 | c.643T>C | p.Ser215Pro | missense_variant | 6/12 | ||
CDC20B | NM_001145734.2 | c.643T>C | p.Ser215Pro | missense_variant | 6/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20B | ENST00000381375.7 | c.643T>C | p.Ser215Pro | missense_variant | 6/12 | 1 | NM_001170402.1 | A1 | |
CDC20B | ENST00000296733.5 | c.643T>C | p.Ser215Pro | missense_variant | 6/12 | 1 | P4 | ||
CDC20B | ENST00000322374.10 | c.643T>C | p.Ser215Pro | missense_variant | 6/11 | 1 | |||
CDC20B | ENST00000513180.5 | c.643T>C | p.Ser215Pro | missense_variant, NMD_transcript_variant | 6/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000805 AC: 20AN: 248374Hom.: 0 AF XY: 0.0000521 AC XY: 7AN XY: 134346
GnomAD4 exome AF: 0.000140 AC: 201AN: 1433130Hom.: 0 Cov.: 28 AF XY: 0.000131 AC XY: 93AN XY: 711566
GnomAD4 genome AF: 0.000105 AC: 16AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.643T>C (p.S215P) alteration is located in exon 6 (coding exon 6) of the CDC20B gene. This alteration results from a T to C substitution at nucleotide position 643, causing the serine (S) at amino acid position 215 to be replaced by a proline (P). 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