Variant 5-55172296-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001170402.1(CDC20B):c.126+292T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 325,882 control chromosomes in the GnomAD database, including 13,700 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 0.24 ( 5275 hom., cov: 32)

Exomes 𝑓: 0.30 ( 8425 hom. )

Consequence

CDC20B
NM_001170402.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0850

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:

MIR449C (HGNC:37302): (microRNA 449c) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR449C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
CDC20B	NM_001170402.1 linkuse as main transcript	c.126+292T>A	intron_variant		ENST00000381375.7
MIR449C	NR_031572.1 linkuse as main transcript	n.58T>A	non_coding_transcript_exon_variant	1/1
CDC20B	NM_001145734.2 linkuse as main transcript	c.126+292T>A	intron_variant
CDC20B	NM_152623.2 linkuse as main transcript	c.126+292T>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC20B	ENST00000381375.7 linkuse as main transcript	c.126+292T>A		intron_variant		1	NM_001170402.1	A1	Q86Y33-1
MIR449C	ENST00000516047.1 linkuse as main transcript	n.58T>A		mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

36065

AN:

151964

Hom.:

5272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0603

Gnomad AMI

AF:

0.484

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.355

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.197

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.233

GnomAD3 exomes

AF:

0.300

AC:

9047

AN:

30206

Hom.:

1498

AF XY:

0.306

AC XY:

4493

AN XY:

14672

show subpopulations

Gnomad AFR exome

AF:

0.0584

Gnomad AMR exome

AF:

0.363

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.367

Gnomad SAS exome

AF:

0.260

Gnomad FIN exome

AF:

0.219

Gnomad NFE exome

AF:

0.328

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.300

AC:

52172

AN:

173798

Hom.:

8425

Cov.:

AF XY:

0.296

AC XY:

27482

AN XY:

92836

show subpopulations

Gnomad4 AFR exome

AF:

0.0626

Gnomad4 AMR exome

AF:

0.360

Gnomad4 ASJ exome

AF:

0.246

Gnomad4 EAS exome

AF:

0.384

Gnomad4 SAS exome

AF:

0.260

Gnomad4 FIN exome

AF:

0.216

Gnomad4 NFE exome

AF:

0.321

Gnomad4 OTH exome

AF:

0.274

GnomAD4 genome

AF:

0.237

AC:

36078

AN:

152084

Hom.:

5275

Cov.:

AF XY:

0.233

AC XY:

17344

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.0602

Gnomad4 AMR

AF:

0.319

Gnomad4 ASJ

AF:

0.243

Gnomad4 EAS

AF:

0.355

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.317

Gnomad4 OTH

AF:

0.236

Alfa

AF:

0.274

Hom.:

762

Bravo

AF:

0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

2.9

DANN

Benign

0.70

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over