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GeneBe

17-65750713-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001199165.4(CEP112):c.2406G>A(p.Lys802=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 1,613,954 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 27 hom. )

Consequence

CEP112
NM_001199165.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.907
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-65750713-C-T is Benign according to our data. Variant chr17-65750713-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648108.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.907 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CEP112NM_001199165.4 linkuse as main transcriptc.2406G>A p.Lys802= synonymous_variant 22/27 ENST00000535342.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CEP112ENST00000535342.7 linkuse as main transcriptc.2406G>A p.Lys802= synonymous_variant 22/272 NM_001199165.4 P1Q8N8E3-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00367
AC:
558
AN:
152080
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000525
Gnomad ASJ
AF:
0.00375
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00414
Gnomad FIN
AF:
0.0287
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00290
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.00473
AC:
1188
AN:
251300
Hom.:
16
AF XY:
0.00504
AC XY:
685
AN XY:
135816
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.000434
Gnomad ASJ exome
AF:
0.00318
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00454
Gnomad FIN exome
AF:
0.0273
Gnomad NFE exome
AF:
0.00323
Gnomad OTH exome
AF:
0.00604
GnomAD4 exome
AF:
0.00280
AC:
4097
AN:
1461756
Hom.:
27
Cov.:
30
AF XY:
0.00289
AC XY:
2101
AN XY:
727198
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
Gnomad4 AMR exome
AF:
0.000447
Gnomad4 ASJ exome
AF:
0.00386
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00390
Gnomad4 FIN exome
AF:
0.0266
Gnomad4 NFE exome
AF:
0.00181
Gnomad4 OTH exome
AF:
0.00295
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00367
AC:
558
AN:
152198
Hom.:
4
Cov.:
32
AF XY:
0.00485
AC XY:
361
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.000337
Gnomad4 AMR
AF:
0.000524
Gnomad4 ASJ
AF:
0.00375
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00414
Gnomad4 FIN
AF:
0.0287
Gnomad4 NFE
AF:
0.00290
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.00267
Hom.:
2
Bravo
AF:
0.00143
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.00153
EpiControl
AF:
0.00237

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2024CEP112: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
Cadd
Benign
6.5
Dann
Benign
0.71

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs144305706; hg19: chr17-63746831; COSMIC: COSV58067648; API