chr5-55119856-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.1404G>T(p.Lys468Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,614,088 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 (★).
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.1404G>T | p.Lys468Asn | missense_variant | 11/12 | ENST00000381375.7 | |
CDC20B | NM_152623.2 | c.1404G>T | p.Lys468Asn | missense_variant | 11/12 | ||
CDC20B | NM_001145734.2 | c.1278G>T | p.Lys426Asn | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20B | ENST00000381375.7 | c.1404G>T | p.Lys468Asn | missense_variant | 11/12 | 1 | NM_001170402.1 | A1 | |
CDC20B | ENST00000296733.5 | c.1404G>T | p.Lys468Asn | missense_variant | 11/12 | 1 | P4 | ||
CDC20B | ENST00000322374.10 | c.1278G>T | p.Lys426Asn | missense_variant | 10/11 | 1 | |||
CDC20B | ENST00000513180.5 | c.*371G>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251152Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135726
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461782Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727194
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2022 | The c.1404G>T (p.K468N) alteration is located in exon 11 (coding exon 11) of the CDC20B gene. This alteration results from a G to T substitution at nucleotide position 1404, causing the lysine (K) at amino acid position 468 to be replaced by an asparagine (N). 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