rs11616761

chr13-114255036-C-Achr13-114255036-C-G

Variant summary

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

The NM_001078645.3(CDC16):c.1098-2042C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 152,200 control chromosomes in the GnomAD database, including 427 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 0.068 (427 hom., cov: 32)
• Consequence: CDC16 NM_001078645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

CDC16 (HGNC:1720): (cell division cycle 16) The protein encoded by this gene functions as a protein ubiquitin ligase and is a component of the multiprotein APC complex. The APC complex is a cyclin degradation system that governs exit from mitosis by targeting cell cycle proteins for degredation by the 26S proteasome. Each component protein of the APC complex is highly conserved among eukaryotic organisms. This protein, and other APC complex proteins, contain a tetratricopeptide repeat (TPR) domain; a protein domain that is often involved in protein-protein interactions and the assembly of multiprotein complexes. Multiple alternatively spliced transcript variants, encoding distinct proteins, have been identified. [provided by RefSeq, Jan 2016]

LOC105370384 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDC16	NM_001078645.3	c.1098-2042C>A		intron_variant		ENST00000356221.8
LOC105370384	XR_007063887.1	n.1092-3700G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC16	ENST00000356221.8	c.1098-2042C>A		intron_variant		1	NM_001078645.3	A1

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10420 AN: 152082 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0825

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0842

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0685 AC: 10424 AN: 152200 Hom.: 427 Cov.: 32 AF XY: 0.0675 AC XY: 5018 AN XY: 74394

Gnomad4 AFR AF: 0.0392

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.0825

Gnomad4 NFE AF: 0.0842

Gnomad4 OTH AF: 0.0779

Alfa AF: 0.0814 Hom.: 820

Bravo AF: 0.0656

Asia WGS AF: 0.0310 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.6
Dann	Benign	0.59

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: rs11616761; hg19: chr13-115020511;