rs16941640

chr17-47187155-T-Achr17-47187155-T-C

Variant summary

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

The NM_001256.6(CDC27):c.27+1991A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 152,196 control chromosomes in the GnomAD database, including 572 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 0.081 (572 hom., cov: 32)
• Consequence: CDC27 NM_001256.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

CDC27 (HGNC:1728): (cell division cycle 27) The protein encoded by this gene shares strong similarity with Saccharomyces cerevisiae protein Cdc27, and the gene product of Schizosaccharomyces pombe nuc 2. This protein is a component of the anaphase-promoting complex (APC), which is composed of eight protein subunits and is highly conserved in eukaryotic cells. This complex catalyzes the formation of cyclin B-ubiquitin conjugate, which is responsible for the ubiquitin-mediated proteolysis of B-type cyclins. The protein encoded by this gene and three other members of the APC complex contain tetratricopeptide (TPR) repeats, which are important for protein-protein interactions. This protein was shown to interact with mitotic checkpoint proteins including Mad2, p55CDC and BUBR1, and it may thus be involved in controlling the timing of mitosis. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 2, 22 and Y. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDC27	NM_001256.6	c.27+1991A>T		intron_variant		ENST00000066544.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC27	ENST00000066544.8	c.27+1991A>T		intron_variant		1	NM_001256.6	P5

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12268 AN: 152078 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0807 AC: 12284 AN: 152196 Hom.: 572 Cov.: 32 AF XY: 0.0809 AC XY: 6019 AN XY: 74424

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0750

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0776

Alfa AF: 0.0241 Hom.: 20

Bravo AF: 0.0799

Asia WGS AF: 0.0530 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.10
Dann	Benign	0.30

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: rs16941640; hg19: chr17-45264521;