Variant 18-13015390-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_032142.4(CEP192):c.582C>G(p.His194Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,549,756 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0049 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0071 ( 45 hom. )

Consequence

CEP192
NM_032142.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0490

Variant links:

Genes affected

CEP192 (HGNC:25515): (centrosomal protein 192) Enables phosphatase binding activity. Involved in centrosome-templated microtubule nucleation; mitotic spindle assembly; and protein localization to centrosome. Located in centriole; centrosome; and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

CEP192 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0029313564).

BP6

Variant 18-13015390-C-G is Benign according to our data. Variant chr18-13015390-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2648604.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 45 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP192	NM_032142.4 linkuse as main transcript	c.582C>G	p.His194Gln	missense_variant	6/45	ENST00000506447.5	NP_115518.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP192	ENST00000506447.5 linkuse as main transcript	c.582C>G	p.His194Gln	missense_variant	6/45	5	NM_032142.4	ENSP00000427550	P1	Q8TEP8-3
CEP192	ENST00000513432.5 linkuse as main transcript	c.249C>G	p.His83Gln	missense_variant, NMD_transcript_variant	3/39	1		ENSP00000424671
CEP192	ENST00000589596.5 linkuse as main transcript	c.582C>G	p.His194Gln	missense_variant	6/18	2		ENSP00000466258
CEP192	ENST00000325971.12 linkuse as main transcript	c.-634C>G		5_prime_UTR_variant	6/44	5		ENSP00000317156

Frequencies

GnomAD3 genomes

AF:

0.00489

AC:

744

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00124

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.00904

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00811

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00508

AC:

781

AN:

153844

Hom.:

AF XY:

0.00508

AC XY:

415

AN XY:

81620

show subpopulations

Gnomad AFR exome

AF:

0.00164

Gnomad AMR exome

AF:

0.000974

Gnomad ASJ exome

AF:

0.000118

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00286

Gnomad FIN exome

AF:

0.00977

Gnomad NFE exome

AF:

0.00849

Gnomad OTH exome

AF:

0.00533

GnomAD4 exome

AF:

0.00711

AC:

9935

AN:

1397418

Hom.:

Cov.:

AF XY:

0.00697

AC XY:

4806

AN XY:

689296

show subpopulations

Gnomad4 AFR exome

AF:

0.000983

Gnomad4 AMR exome

AF:

0.000925

Gnomad4 ASJ exome

AF:

0.0000795

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.00309

Gnomad4 FIN exome

AF:

0.00983

Gnomad4 NFE exome

AF:

0.00822

Gnomad4 OTH exome

AF:

0.00470

GnomAD4 genome

AF:

0.00488

AC:

744

AN:

152338

Hom.:

Cov.:

AF XY:

0.00443

AC XY:

330

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00124

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00311

Gnomad4 FIN

AF:

0.00904

Gnomad4 NFE

AF:

0.00811

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00678

Hom.:

Bravo

AF:

0.00413

TwinsUK

AF:

0.00701

AC:

ALSPAC

AF:

0.00701

AC:

ESP6500AA

AF:

0.000723

AC:

ESP6500EA

AF:

0.00880

AC:

ExAC

AF:

0.00400

AC:

Asia WGS

AF:

0.00115

AC:

AN:

3478

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

CEP192: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.68

CADD

Benign

1.1

DANN

Benign

0.94

DEOGEN2

Benign

0.027

T;.

Eigen

Benign

-0.84

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.076

LIST_S2

Benign

0.64

T;T

M_CAP

Benign

0.0075

MetaRNN

Benign

0.0029

T;T

MetaSVM

Benign

-0.94

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.71

.;N

REVEL

Benign

0.036

Sift

Benign

0.40

.;T

Sift4G

Benign

0.37

T;T

Vest4

0.23

MutPred

0.085

Gain of relative solvent accessibility (P = 0.1012);Gain of relative solvent accessibility (P = 0.1012);

MVP

0.14

MPC

0.13

ClinPred

0.0077

GERP RS

0.24

Varity_R

0.030

gMVP

0.063

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over