rs336081

Variant names:

• chr5-55137565-G-A
• rs336081
• NM_001170402.1:c.580+2749C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-55137565-G-A
• chr5-55137565-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170402.1(CDC20B):​c.580+2749C>T variant causes a intron 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 NM_001170402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 8 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001170402.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC20B	NM_001170402.1	MANE Select	c.580+2749C>T		intron	N/A	NP_001163873.1	Q86Y33-1
	CDC20B	NM_152623.2		c.580+2749C>T		intron	N/A	NP_689836.2	Q86Y33-2
	CDC20B	NM_001145734.2		c.580+2749C>T		intron	N/A	NP_001139206.2	Q86Y33-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC20B	ENST00000381375.7	TSL:1 MANE Select	c.580+2749C>T		intron	N/A	ENSP00000370781.2	Q86Y33-1
	CDC20B	ENST00000296733.5	TSL:1	c.580+2749C>T		intron	N/A	ENSP00000296733.1	Q86Y33-2
	CDC20B	ENST00000322374.10	TSL:1	c.580+2749C>T		intron	N/A	ENSP00000315720.6	Q86Y33-3

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90913 AN: 151896 Hom.: 27544 Cov.: 32

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

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.: 0 AF XY: 0.612 AC XY: 106018 AN XY: 173332

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

GnomAD4 genome AF: 0.598 AC: 90978 AN: 152016 Hom.: 27563 Cov.: 32 AF XY: 0.595 AC XY: 44198 AN XY: 74288

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

Alfa AF: 0.611 Hom.: 13046

Bravo AF: 0.605

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.067
DANN	Benign	0.31
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs336081; hg19: chr5-54433393; COSMIC: COSV104393354;