chr5-55124924-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001170402.1(CDC20B):c.1094C>T(p.Pro365Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,614,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC20B | NM_001170402.1 | c.1094C>T | p.Pro365Leu | missense_variant | 9/12 | ENST00000381375.7 | |
CDC20B | NM_152623.2 | c.1094C>T | p.Pro365Leu | missense_variant | 9/12 | ||
CDC20B | NM_001145734.2 | c.1094C>T | p.Pro365Leu | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20B | ENST00000381375.7 | c.1094C>T | p.Pro365Leu | missense_variant | 9/12 | 1 | NM_001170402.1 | A1 | |
CDC20B | ENST00000296733.5 | c.1094C>T | p.Pro365Leu | missense_variant | 9/12 | 1 | P4 | ||
CDC20B | ENST00000322374.10 | c.1094C>T | p.Pro365Leu | missense_variant | 9/11 | 1 | |||
CDC20B | ENST00000513180.5 | c.*61C>T | 3_prime_UTR_variant, NMD_transcript_variant | 10/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251118Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135700
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461858Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 727230
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.1094C>T (p.P365L) alteration is located in exon 9 (coding exon 9) of the CDC20B gene. This alteration results from a C to T substitution at nucleotide position 1094, causing the proline (P) at amino acid position 365 to be replaced by a leucine (L). 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