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GeneBe

17-65637177-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_001199165.4(CEP112):c.2811G>T(p.Leu937=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00214 in 1,613,708 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0094 ( 20 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 32 hom. )

Consequence

CEP112
NM_001199165.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.113
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 -13 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=-0.25).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-65637177-C-A is Benign according to our data. Variant chr17-65637177-C-A is described in ClinVar as [Benign]. Clinvar id is 781327.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=0.113 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00939 (1430/152266) while in subpopulation AFR AF= 0.0312 (1296/41558). AF 95% confidence interval is 0.0298. There are 20 homozygotes in gnomad4. There are 693 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
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 19 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CEP112NM_001199165.4 linkuse as main transcriptc.2811G>T p.Leu937= synonymous_variant 26/27 ENST00000535342.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CEP112ENST00000535342.7 linkuse as main transcriptc.2811G>T p.Leu937= synonymous_variant 26/272 NM_001199165.4 P1Q8N8E3-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00940
AC:
1430
AN:
152148
Hom.:
19
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0313
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00439
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00228
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000426
Gnomad OTH
AF:
0.0110
GnomAD3 exomes
AF:
0.00333
AC:
836
AN:
251146
Hom.:
10
AF XY:
0.00270
AC XY:
367
AN XY:
135724
show subpopulations
Gnomad AFR exome
AF:
0.0333
Gnomad AMR exome
AF:
0.00367
Gnomad ASJ exome
AF:
0.00258
Gnomad EAS exome
AF:
0.0000545
Gnomad SAS exome
AF:
0.00206
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000396
Gnomad OTH exome
AF:
0.00539
GnomAD4 exome
AF:
0.00138
AC:
2016
AN:
1461442
Hom.:
32
Cov.:
30
AF XY:
0.00133
AC XY:
968
AN XY:
727050
show subpopulations
Gnomad4 AFR exome
AF:
0.0301
Gnomad4 AMR exome
AF:
0.00436
Gnomad4 ASJ exome
AF:
0.00222
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00220
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000304
Gnomad4 OTH exome
AF:
0.00318
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00939
AC:
1430
AN:
152266
Hom.:
20
Cov.:
32
AF XY:
0.00931
AC XY:
693
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0312
Gnomad4 AMR
AF:
0.00438
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00228
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000426
Gnomad4 OTH
AF:
0.0109
Alfa
AF:
0.00332
Hom.:
6
Bravo
AF:
0.0115
Asia WGS
AF:
0.00375
AC:
13
AN:
3478
EpiCase
AF:
0.000654
EpiControl
AF:
0.000415

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 14, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.25
Cadd
Benign
3.7
Dann
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs75033823; hg19: chr17-63633295; API