dbSNP rs2107654: CEP112:c.2864+169A>G (chr17-65636955-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001199165.4(CEP112):c.2864+169A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 604,246 control chromosomes in the GnomAD database, including 73,149 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 0.48 ( 17763 hom., cov: 31)

Exomes 𝑓: 0.49 ( 55386 hom. )

Consequence

CEP112
NM_001199165.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.951

Publications

11 publications found

Variant links:

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)

CEP112 links:

ENSG00000266076 (HGNC:):

ENSG00000266076 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP112	NM_001199165.4 link	c.2864+169A>G		intron_variant	Intron 26 of 26	ENST00000535342.7	NP_001186094.1	Q8N8E3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP112	ENST00000535342.7 link	c.2864+169A>G		intron_variant	Intron 26 of 26	2	NM_001199165.4	ENSP00000442784.2		Q8N8E3-1
ENSG00000266076	ENST00000577662.1 link	n.134+169A>G		intron_variant	Intron 2 of 6	2		ENSP00000462418.1		J3KSC3

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

72987

AN:

151630

Hom.:

17746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.445

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.563

Gnomad ASJ

AF:

0.635

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.502

GnomAD4 exome

AF:

0.491

AC:

222344

AN:

452494

Hom.:

55386

Cov.:

AF XY:

0.491

AC XY:

117515

AN XY:

239302

show subpopulations

African (AFR)

AF:

0.444

AC:

5491

AN:

12380

American (AMR)

AF:

0.529

AC:

10152

AN:

19200

Ashkenazi Jewish (ASJ)

AF:

0.634

AC:

8683

AN:

13704

East Asian (EAS)

AF:

0.514

AC:

15899

AN:

30914

South Asian (SAS)

AF:

0.492

AC:

21322

AN:

43342

European-Finnish (FIN)

AF:

0.506

AC:

16650

AN:

32910

Middle Eastern (MID)

AF:

0.587

AC:

1427

AN:

2432

European-Non Finnish (NFE)

AF:

0.478

AC:

129818

AN:

271692

Other (OTH)

AF:

0.498

AC:

12902

AN:

25920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

5199

10398

15597

20796

25995

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

720

1440

2160

2880

3600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.481

AC:

73033

AN:

151752

Hom.:

17763

Cov.:

AF XY:

0.486

AC XY:

36050

AN XY:

74170

show subpopulations

African (AFR)

AF:

0.445

AC:

18356

AN:

41272

American (AMR)

AF:

0.562

AC:

8583

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.635

AC:

2202

AN:

3466

East Asian (EAS)

AF:

0.463

AC:

2379

AN:

5142

South Asian (SAS)

AF:

0.483

AC:

2328

AN:

4820

European-Finnish (FIN)

AF:

0.510

AC:

5376

AN:

10544

Middle Eastern (MID)

AF:

0.589

AC:

172

AN:

292

European-Non Finnish (NFE)

AF:

0.473

AC:

32133

AN:

67934

Other (OTH)

AF:

0.507

AC:

1068

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1947

3894

5840

7787

9734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

662

1324

1986

2648

3310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.482

Hom.:

75598

Bravo

AF:

0.478

Asia WGS

AF:

0.510

AC:

1774

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.0

(source)

DANN

Benign

0.57

PhyloP100

0.95

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over