rs2241008

Positions:

• chr17-65902039-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001199165.4(CEP112):​c.2163+113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 418,364 control chromosomes in the GnomAD database, including 133,357 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 0.75 (38740 hom., cov: 20)
  • Exomes 𝑓: 0.81 (94617 hom.)
• Consequence: CEP112 NM_001199165.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.25

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]

LOC105371867 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP112	NM_001199165.4	c.2163+113G>A		intron_variant		ENST00000535342.7
LOC105371867	XR_001752977.3	n.265-9806C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP112	ENST00000535342.7	c.2163+113G>A		intron_variant		2	NM_001199165.4	P1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 98916 AN: 132140 Hom.: 38730 Cov.: 20

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.769

GnomAD4 exome AF: 0.805 AC: 230374 AN: 286126 Hom.: 94617 AF XY: 0.808 AC XY: 121070 AN XY: 149832

Gnomad4 AFR exome AF: 0.599

Gnomad4 AMR exome AF: 0.726

Gnomad4 ASJ exome AF: 0.836

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.788

Gnomad4 FIN exome AF: 0.711

Gnomad4 NFE exome AF: 0.867

Gnomad4 OTH exome AF: 0.795

GnomAD4 genome AF: 0.748 AC: 98969 AN: 132238 Hom.: 38740 Cov.: 20 AF XY: 0.739 AC XY: 46056 AN XY: 62348

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.765

Alfa AF: 0.854 Hom.: 65919

Bravo AF: 0.730

Asia WGS AF: 0.549 AC: 1903 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	21
DANN	Benign	0.87

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: rs2241008; hg19: chr17-63898157;