rs232099

Variant names:

• chr17-65717752-C-T
• rs232099
• NM_001199165.4:c.2607+25316G>A

Variant summary

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

The NM_001199165.4(CEP112):​c.2607+25316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,058 control chromosomes in the GnomAD database, including 17,413 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 0.47 (17413 hom., cov: 32)
• Consequence: CEP112 NM_001199165.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• spermatogenic failure 44

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP112	NM_001199165.4	c.2607+25316G>A		intron_variant	Intron 23 of 26	ENST00000535342.7	NP_001186094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP112	ENST00000535342.7	c.2607+25316G>A		intron_variant	Intron 23 of 26	2	NM_001199165.4	ENSP00000442784.2

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70916 AN: 151938 Hom.: 17374 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.467 AC: 71001 AN: 152058 Hom.: 17413 Cov.: 32 AF XY: 0.464 AC XY: 34525 AN XY: 74352

African (AFR) AF: 0.610 AC: 25291 AN: 41466

American (AMR) AF: 0.399 AC: 6091 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1597 AN: 5176

South Asian (SAS) AF: 0.376 AC: 1812 AN: 4822

European-Finnish (FIN) AF: 0.438 AC: 4630 AN: 10570

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27936 AN: 67966

Other (OTH) AF: 0.490 AC: 1035 AN: 2114

Alfa AF: 0.436 Hom.: 1837

Bravo AF: 0.472

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.035
DANN	Benign	0.20
PhyloP100		-0.55
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: rs232099; hg19: chr17-63713870;