chr5-55124997-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001170402.1(CDC20B):c.1021G>A(p.Asp341Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000403 in 1,613,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000040 ( 0 hom. )
Consequence
CDC20B
NM_001170402.1 missense
NM_001170402.1 missense
Scores
7
6
4
Clinical Significance
Conservation
PhyloP100: 4.73
Genes affected
CDC20B (HGNC:24222): (cell division cycle 20B) Predicted to enable anaphase-promoting complex binding activity and ubiquitin ligase activator activity. Predicted to be involved in anaphase-promoting complex-dependent catabolic process and positive regulation of anaphase-promoting complex-dependent catabolic process. Predicted to be part of anaphase-promoting complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.779
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC20B | NM_001170402.1 | c.1021G>A | p.Asp341Asn | missense_variant | 9/12 | ENST00000381375.7 | |
CDC20B | NM_152623.2 | c.1021G>A | p.Asp341Asn | missense_variant | 9/12 | ||
CDC20B | NM_001145734.2 | c.1021G>A | p.Asp341Asn | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20B | ENST00000381375.7 | c.1021G>A | p.Asp341Asn | missense_variant | 9/12 | 1 | NM_001170402.1 | A1 | |
CDC20B | ENST00000296733.5 | c.1021G>A | p.Asp341Asn | missense_variant | 9/12 | 1 | P4 | ||
CDC20B | ENST00000322374.10 | c.1021G>A | p.Asp341Asn | missense_variant | 9/11 | 1 | |||
CDC20B | ENST00000513180.5 | c.1107G>A | p.Thr369= | synonymous_variant, NMD_transcript_variant | 10/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152200Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
6
AN:
152200
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250976Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135596
GnomAD3 exomes
AF:
AC:
8
AN:
250976
Hom.:
AF XY:
AC XY:
6
AN XY:
135596
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461376Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 726874
GnomAD4 exome
AF:
AC:
59
AN:
1461376
Hom.:
Cov.:
31
AF XY:
AC XY:
33
AN XY:
726874
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74360
GnomAD4 genome
AF:
AC:
6
AN:
152200
Hom.:
Cov.:
32
AF XY:
AC XY:
3
AN XY:
74360
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
AF:
AC:
6
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2022 | The c.1021G>A (p.D341N) alteration is located in exon 9 (coding exon 9) of the CDC20B gene. This alteration results from a G to A substitution at nucleotide position 1021, causing the aspartic acid (D) at amino acid position 341 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;T;D
M_CAP
Benign
T
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D
REVEL
Uncertain
Sift
Pathogenic
D;D;D
Sift4G
Pathogenic
D;D;D
Polyphen
D;D;D
Vest4
MVP
MPC
0.78
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at