rs997651

Variant names:

• chr17-65918265-G-A
• rs997651
• NM_001199165.4:c.1980+9317C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-65918265-G-A
• chr17-65918265-G-T

Variant summary

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

The NM_001199165.4(CEP112):​c.1980+9317C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,540 control chromosomes in the GnomAD database, including 13,337 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 0.41 (13337 hom., cov: 31)
• Consequence: CEP112 NM_001199165.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199165.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP112	NM_001199165.4	MANE Select	c.1980+9317C>T		intron	N/A	NP_001186094.1	Q8N8E3-1
	CEP112	NM_001353129.2		c.1983+9317C>T		intron	N/A	NP_001340058.1
	CEP112	NM_001353127.2		c.1980+9317C>T		intron	N/A	NP_001340056.1	Q8N8E3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP112	ENST00000535342.7	TSL:2 MANE Select	c.1980+9317C>T		intron	N/A	ENSP00000442784.2	Q8N8E3-1
	CEP112	ENST00000537949.5	TSL:1	c.1854+9317C>T		intron	N/A	ENSP00000440775.1	F5GYE8
	CEP112	ENST00000859226.1		c.2079+9317C>T		intron	N/A	ENSP00000529285.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62466 AN: 151422 Hom.: 13307 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.413 AC: 62543 AN: 151540 Hom.: 13337 Cov.: 31 AF XY: 0.415 AC XY: 30709 AN XY: 74016

African (AFR) AF: 0.458 AC: 18884 AN: 41240

American (AMR) AF: 0.473 AC: 7193 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1622 AN: 3456

East Asian (EAS) AF: 0.193 AC: 998 AN: 5162

South Asian (SAS) AF: 0.648 AC: 3123 AN: 4816

European-Finnish (FIN) AF: 0.279 AC: 2925 AN: 10470

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26441 AN: 67874

Other (OTH) AF: 0.437 AC: 922 AN: 2110

Alfa AF: 0.408 Hom.: 6685

Bravo AF: 0.419

Asia WGS AF: 0.436 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.56
PhyloP100		-0.56
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: rs997651; hg19: chr17-63914383;