rs7209395

Variant names:

• chr17-66137608-T-C
• rs7209395
• NM_001199165.4:c.471-4845A>G

Variant summary

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

The NM_001199165.4(CEP112):​c.471-4845A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,088 control chromosomes in the GnomAD database, including 3,721 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 0.21 (3721 hom., cov: 32)
• Consequence: CEP112 NM_001199165.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP112	NM_001199165.4	c.471-4845A>G		intron_variant	Intron 4 of 26	ENST00000535342.7	NP_001186094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP112	ENST00000535342.7	c.471-4845A>G		intron_variant	Intron 4 of 26	2	NM_001199165.4	ENSP00000442784.2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32107 AN: 151972 Hom.: 3721 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.211 AC: 32100 AN: 152088 Hom.: 3721 Cov.: 32 AF XY: 0.211 AC XY: 15693 AN XY: 74360

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.226

Alfa AF: 0.236 Hom.: 4080

Bravo AF: 0.202

Asia WGS AF: 0.0700 AC: 247 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.69

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: rs7209395; hg19: chr17-64133726;