NM_001256875.2:c.584+559G>A

Variant names:

• chr1-37703906-G-A
• rs3790623
• NM_001256875.2:c.584+559G>A

Variant summary

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

The NM_001256875.2(CDCA8):​c.584+559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,908 control chromosomes in the GnomAD database, including 4,386 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 0.23 (4386 hom., cov: 31)
• Consequence: CDCA8 NM_001256875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 6 publications found

Genes affected

CDCA8 (HGNC:14629): (cell division cycle associated 8) This gene encodes a component of the chromosomal passenger complex. This complex is an essential regulator of mitosis and cell division. This protein is cell-cycle regulated and is required for chromatin-induced microtubule stabilization and spindle formation. Alternate splicing results in multiple transcript variants. Pseudgenes of this gene are found on chromosomes 7, 8 and 16. [provided by RefSeq, Apr 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256875.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDCA8	NM_001256875.2	MANE Select	c.584+559G>A		intron	N/A	NP_001243804.1
	CDCA8	NM_018101.4		c.584+559G>A		intron	N/A	NP_060571.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDCA8	ENST00000373055.6	TSL:1 MANE Select	c.584+559G>A		intron	N/A	ENSP00000362146.1
	CDCA8	ENST00000327331.2	TSL:1	c.584+559G>A		intron	N/A	ENSP00000316121.2

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35337 AN: 151790 Hom.: 4393 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.233 AC: 35339 AN: 151908 Hom.: 4386 Cov.: 31 AF XY: 0.232 AC XY: 17224 AN XY: 74220

African (AFR) AF: 0.160 AC: 6620 AN: 41416

American (AMR) AF: 0.263 AC: 4017 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1020 AN: 5178

South Asian (SAS) AF: 0.252 AC: 1211 AN: 4798

European-Finnish (FIN) AF: 0.227 AC: 2397 AN: 10548

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18707 AN: 67932

Other (OTH) AF: 0.244 AC: 515 AN: 2108

Alfa AF: 0.261 Hom.: 9061

Bravo AF: 0.230

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.36
DANN	Benign	0.77
PhyloP100		-2.9
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: rs3790623; hg19: chr1-38169578;