rs8074751

chr17-65646424-G-A

Variant summary

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

The NM_001199165.4(CEP112):c.2698-5359C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,102 control chromosomes in the GnomAD database, including 38,532 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 0.70 (38532 hom., cov: 32)
• Consequence: CEP112 NM_001199165.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP112	NM_001199165.4	c.2698-5359C>T		intron_variant		ENST00000535342.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP112	ENST00000535342.7	c.2698-5359C>T		intron_variant		2	NM_001199165.4	P1

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105980 AN: 151984 Hom.: 38476 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.697 AC: 106089 AN: 152102 Hom.: 38532 Cov.: 32 AF XY: 0.701 AC XY: 52077 AN XY: 74340

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.680

Alfa AF: 0.604 Hom.: 42160

Bravo AF: 0.718

Asia WGS AF: 0.791 AC: 2748 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	2.7
Dann	Benign	0.33

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: rs8074751; hg19: chr17-63642542;