Variant 1-37708311-TTTC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001256875.2(CDCA8):c.799-8_799-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,610,346 control chromosomes in the GnomAD database, including 45,565 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars).

Frequency

Genomes: 𝑓 0.24 ( 5200 hom., cov: 26)

Exomes 𝑓: 0.21 ( 40365 hom. )

Consequence

CDCA8
NM_001256875.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.197

Variant links:

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]

CDCA8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDCA8	NM_001256875.2 linkuse as main transcript	c.799-8_799-6del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000373055.6
CDCA8	NM_018101.4 linkuse as main transcript	c.799-8_799-6del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDCA8	ENST00000373055.6 linkuse as main transcript	c.799-8_799-6del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_001256875.2	P1
CDCA8	ENST00000327331.2 linkuse as main transcript	c.799-8_799-6del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		P1

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

36566

AN:

151818

Hom.:

5179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.253

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.686

Gnomad SAS

AF:

0.327

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.239

GnomAD3 exomes

AF:

0.284

AC:

71079

AN:

250248

Hom.:

12973

AF XY:

0.276

AC XY:

37307

AN XY:

135408

show subpopulations

Gnomad AFR exome

AF:

0.250

Gnomad AMR exome

AF:

0.425

Gnomad ASJ exome

AF:

0.275

Gnomad EAS exome

AF:

0.705

Gnomad SAS exome

AF:

0.321

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.182

Gnomad OTH exome

AF:

0.240

GnomAD4 exome

AF:

0.213

AC:

310048

AN:

1458408

Hom.:

40365

AF XY:

0.214

AC XY:

155593

AN XY:

725682

show subpopulations

Gnomad4 AFR exome

AF:

0.251

Gnomad4 AMR exome

AF:

0.409

Gnomad4 ASJ exome

AF:

0.274

Gnomad4 EAS exome

AF:

0.671

Gnomad4 SAS exome

AF:

0.312

Gnomad4 FIN exome

AF:

0.220

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.237

GnomAD4 genome

AF:

0.241

AC:

36650

AN:

151938

Hom.:

5200

Cov.:

AF XY:

0.248

AC XY:

18405

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.253

Gnomad4 AMR

AF:

0.314

Gnomad4 ASJ

AF:

0.278

Gnomad4 EAS

AF:

0.686

Gnomad4 SAS

AF:

0.327

Gnomad4 FIN

AF:

0.225

Gnomad4 NFE

AF:

0.180

Gnomad4 OTH

AF:

0.248

Alfa

AF:

0.220

Hom.:

698

Bravo

AF:

0.253

Asia WGS

AF:

0.473

AC:

1642

AN:

3476

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Neutrophil inclusion bodies

Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

Phenosystems SA

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over