chr17-47180251-T-C

Variant names:

• chr17-47180251-T-C
• rs764792
• NM_001256.6:c.103+1311A>G

Variant summary

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

The NM_001256.6(CDC27):​c.103+1311A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,080 control chromosomes in the GnomAD database, including 10,066 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 0.35 (10066 hom., cov: 31)
• Consequence: CDC27 NM_001256.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC27	NM_001256.6	c.103+1311A>G		intron_variant	Intron 2 of 18	ENST00000066544.8	NP_001247.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC27	ENST00000066544.8	c.103+1311A>G		intron_variant	Intron 2 of 18	1	NM_001256.6	ENSP00000066544.3

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53769 AN: 151962 Hom.: 10060 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.354 AC: 53795 AN: 152080 Hom.: 10066 Cov.: 31 AF XY: 0.352 AC XY: 26165 AN XY: 74330

African (AFR) AF: 0.262 AC: 10881 AN: 41490

American (AMR) AF: 0.427 AC: 6533 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.146 AC: 756 AN: 5184

South Asian (SAS) AF: 0.252 AC: 1213 AN: 4814

European-Finnish (FIN) AF: 0.418 AC: 4420 AN: 10562

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27306 AN: 67964

Other (OTH) AF: 0.366 AC: 774 AN: 2112

Alfa AF: 0.364 Hom.: 1745

Bravo AF: 0.351

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		0.22
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: rs764792; hg19: chr17-45257617;