rs11210838

Variant names:

• chr1-43361519-C-A
• rs11210838
• NM_001255.3:c.1203+274C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

CDC20 Gene-Disease associations (from GenCC):

• oocyte maturation defect 14

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CDC20	NM_001255.3	c.1203+274C>A		intron_variant	Intron 9 of 10	ENST00000310955.11	NP_001246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC20	ENST00000310955.11	c.1203+274C>A		intron_variant	Intron 9 of 10	1	NM_001255.3	ENSP00000308450.5
CDC20	ENST00000372462.1	c.1203+274C>A		intron_variant	Intron 8 of 9	1		ENSP00000361540.1
CDC20	ENST00000482046.1	n.188+274C>A		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.0273 AC: 1136 AN: 41552

American (AMR) AF: 0.0940 AC: 1437 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5188

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4824

European-Finnish (FIN) AF: 0.107 AC: 1138 AN: 10608

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9525 AN: 67990

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.116 Hom.: 2129

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
PhyloP100		1.2
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: rs11210838; hg19: chr1-43827190;