dbSNP rs336081: CDC20B:n.*10C>T (chr5-55137565-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000507931.1(CDC20B):n.*10C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 456,418 control chromosomes in the GnomAD database, including 86,313 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.60 ( 27563 hom., cov: 32)

Exomes 𝑓: 0.62 ( 58750 hom. )

Consequence

CDC20B
ENST00000507931.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.222

Publications

8 publications found

Variant links:

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]

CDC20B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CDC20B	NM_001170402.1 link	c.580+2749C>T	intron_variant	Intron 5 of 11	ENST00000381375.7	NP_001163873.1	Q86Y33-1
CDC20B	NM_152623.2 link	c.580+2749C>T	intron_variant	Intron 5 of 11		NP_689836.2	Q86Y33-2
CDC20B	NM_001145734.2 link	c.580+2749C>T	intron_variant	Intron 5 of 10		NP_001139206.2	Q86Y33-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC20B	ENST00000381375.7 link	c.580+2749C>T		intron_variant	Intron 5 of 11	1	NM_001170402.1	ENSP00000370781.2		Q86Y33-1

Frequencies

GnomAD3 genomes

AF:

0.599

AC:

90913

AN:

151896

Hom.:

27544

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.660

Gnomad AMR

AF:

0.690

Gnomad ASJ

AF:

0.656

Gnomad EAS

AF:

0.550

Gnomad SAS

AF:

0.548

Gnomad FIN

AF:

0.555

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.637

Gnomad OTH

AF:

0.607

GnomAD2 exomes

AF:

0.623

AC:

85391

AN:

137002

AF XY:

0.617

show subpopulations

Gnomad AFR exome

AF:

0.505

Gnomad AMR exome

AF:

0.740

Gnomad ASJ exome

AF:

0.657

Gnomad EAS exome

AF:

0.528

Gnomad FIN exome

AF:

0.559

Gnomad NFE exome

AF:

0.636

Gnomad OTH exome

AF:

0.636

GnomAD4 exome

AF:

0.618

AC:

188105

AN:

304402

Hom.:

58750

Cov.:

AF XY:

0.612

AC XY:

106018

AN XY:

173332

show subpopulations

African (AFR)

AF:

0.513

AC:

4430

AN:

8628

American (AMR)

AF:

0.741

AC:

20226

AN:

27282

Ashkenazi Jewish (ASJ)

AF:

0.658

AC:

7103

AN:

10790

East Asian (EAS)

AF:

0.537

AC:

4942

AN:

9210

South Asian (SAS)

AF:

0.551

AC:

32932

AN:

59742

European-Finnish (FIN)

AF:

0.553

AC:

7078

AN:

12790

Middle Eastern (MID)

AF:

0.613

AC:

1706

AN:

2782

European-Non Finnish (NFE)

AF:

0.635

AC:

100940

AN:

158942

Other (OTH)

AF:

0.614

AC:

8748

AN:

14236

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

4504

9008

13512

18016

22520

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

552

1104

1656

2208

2760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.598

AC:

90978

AN:

152016

Hom.:

27563

Cov.:

AF XY:

0.595

AC XY:

44198

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.517

AC:

21405

AN:

41434

American (AMR)

AF:

0.690

AC:

10540

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.656

AC:

2278

AN:

3472

East Asian (EAS)

AF:

0.549

AC:

2839

AN:

5168

South Asian (SAS)

AF:

0.547

AC:

2636

AN:

4816

European-Finnish (FIN)

AF:

0.555

AC:

5864

AN:

10558

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.637

AC:

43334

AN:

67976

Other (OTH)

AF:

0.610

AC:

1289

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1854

3708

5561

7415

9269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.611

Hom.:

13046

Bravo

AF:

0.605

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.067

(source)

DANN

Benign

0.31

PhyloP100

-0.22

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over