rs11210838

chr1-43361519-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001255.3(CDC20):c.1203+274C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,238 control chromosomes in the GnomAD database, including 913 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 0.094 (913 hom., cov: 32)
• Consequence: CDC20 NM_001255.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

CDC20 (HGNC:1723): (cell division cycle 20) CDC20 appears to act as a regulatory protein interacting with several other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes, nuclear movement prior to anaphase and chromosome separation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDC20	NM_001255.3	c.1203+274C>A		intron_variant		ENST00000310955.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC20	ENST00000310955.11	c.1203+274C>A		intron_variant		1	NM_001255.3	P1
CDC20	ENST00000372462.1	c.1203+274C>A		intron_variant		1		P1
CDC20	ENST00000482046.1	n.188+274C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14277 AN: 152120 Hom.: 912 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.121

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0937 AC: 14272 AN: 152238 Hom.: 913 Cov.: 32 AF XY: 0.0895 AC XY: 6662 AN XY: 74436

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.0940

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.119

Alfa AF: 0.131 Hom.: 1481

Bravo AF: 0.0913

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	15
Dann	Benign	0.81

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

Other links and lift over

dbSNP: rs11210838; hg19: chr1-43827190;