chr5-55119821-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001170402.1(CDC20B):c.1439C>T(p.Ser480Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000744 in 1,613,464 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.1439C>T | p.Ser480Phe | missense_variant | 11/12 | ENST00000381375.7 | |
CDC20B | NM_152623.2 | c.1439C>T | p.Ser480Phe | missense_variant | 11/12 | ||
CDC20B | NM_001145734.2 | c.1313C>T | p.Ser438Phe | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20B | ENST00000381375.7 | c.1439C>T | p.Ser480Phe | missense_variant | 11/12 | 1 | NM_001170402.1 | A1 | |
CDC20B | ENST00000296733.5 | c.1439C>T | p.Ser480Phe | missense_variant | 11/12 | 1 | P4 | ||
CDC20B | ENST00000322374.10 | c.1313C>T | p.Ser438Phe | missense_variant | 10/11 | 1 | |||
CDC20B | ENST00000513180.5 | c.*406C>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250854Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135530
GnomAD4 exome AF: 0.0000766 AC: 112AN: 1461330Hom.: 0 Cov.: 30 AF XY: 0.0000812 AC XY: 59AN XY: 727014
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.1439C>T (p.S480F) alteration is located in exon 11 (coding exon 11) of the CDC20B gene. This alteration results from a C to T substitution at nucleotide position 1439, causing the serine (S) at amino acid position 480 to be replaced by a phenylalanine (F). 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