chr17-65659263-C-T

Position:

• chr17-65659263-C-T

Variant summary

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

The NM_001199165.4(CEP112):​c.2698-18198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,928 control chromosomes in the GnomAD database, including 23,586 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 0.55 (23586 hom., cov: 31)
• Consequence: CEP112 NM_001199165.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745

Genes affected

CEP112 (HGNC:28514): (centrosomal protein 112) This gene encodes a coiled-coil domain containing protein that belongs to the cell division control protein 42 effector protein family. In neurons, it localizes to the cytoplasm of dendrites and is also enriched in the nucleus where it interacts with the RNA polymerase III transcriptional repressor Maf1 to regulate gamma-aminobutyric acid A receptor surface expression. In addition, the protein has been identified as a component of the human centrosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

CEP112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP112	NM_001199165.4	c.2698-18198G>A		intron_variant		ENST00000535342.7	NP_001186094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP112	ENST00000535342.7	c.2698-18198G>A		intron_variant		2	NM_001199165.4	ENSP00000442784.2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83180 AN: 151810 Hom.: 23550 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.548 AC: 83272 AN: 151928 Hom.: 23586 Cov.: 31 AF XY: 0.548 AC XY: 40657 AN XY: 74240

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.531

Alfa AF: 0.493 Hom.: 17682

Bravo AF: 0.563

Asia WGS AF: 0.623 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.64

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: rs9889486; hg19: chr17-63655381;