Variant chr3-101726726-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_024548.4(CEP97):c.176G>A(p.Arg59Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00534 in 1,601,490 control chromosomes in the GnomAD database, including 33 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 Benign (★★).

Frequency

Genomes: 𝑓 0.0043 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0055 ( 32 hom. )

Consequence

CEP97
NM_024548.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.393

Variant links:

Genes affected

CEP97 (HGNC:26244): (centrosomal protein 97) Predicted to enable calmodulin binding activity. Involved in negative regulation of cilium assembly and regulation of mitotic spindle assembly. Located in centriolar satellite and cytosol. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

CEP97 links:

CEP97 (HGNC:):

CEP97 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0071690083).

BP6

Variant 3-101726726-G-A is Benign according to our data. Variant chr3-101726726-G-A is described in ClinVar as [Benign]. Clinvar id is 777375.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 32 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP97	NM_024548.4 linkuse as main transcript	c.176G>A	p.Arg59Gln	missense_variant	2/11	ENST00000341893.8	NP_078824.2	Q8IW35-1
CEP97	NM_001410784.1 linkuse as main transcript	c.176G>A	p.Arg59Gln	missense_variant	2/10		NP_001397713.1
CEP97	NM_001303401.2 linkuse as main transcript	c.176G>A	p.Arg59Gln	missense_variant	2/11		NP_001290330.1	Q8IW35E9PG22B4DGU8
CEP97	NM_001410785.1 linkuse as main transcript	c.176G>A	p.Arg59Gln	missense_variant	2/10		NP_001397714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP97	ENST00000341893.8 linkuse as main transcript	c.176G>A	p.Arg59Gln	missense_variant	2/11	1	NM_024548.4	ENSP00000342510.3		Q8IW35-1

Frequencies

GnomAD3 genomes

AF:

0.00427

AC:

650

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00550

Gnomad ASJ

AF:

0.00923

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00615

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.00502

AC:

1231

AN:

245124

Hom.:

AF XY:

0.00513

AC XY:

681

AN XY:

132696

show subpopulations

Gnomad AFR exome

AF:

0.00126

Gnomad AMR exome

AF:

0.00441

Gnomad ASJ exome

AF:

0.00998

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00359

Gnomad FIN exome

AF:

0.00281

Gnomad NFE exome

AF:

0.00678

Gnomad OTH exome

AF:

0.00757

GnomAD4 exome

AF:

0.00545

AC:

7903

AN:

1449260

Hom.:

Cov.:

AF XY:

0.00550

AC XY:

3965

AN XY:

721496

show subpopulations

Gnomad4 AFR exome

AF:

0.000908

Gnomad4 AMR exome

AF:

0.00469

Gnomad4 ASJ exome

AF:

0.0101

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00379

Gnomad4 FIN exome

AF:

0.00227

Gnomad4 NFE exome

AF:

0.00594

Gnomad4 OTH exome

AF:

0.00549

GnomAD4 genome

AF:

0.00427

AC:

650

AN:

152230

Hom.:

Cov.:

AF XY:

0.00402

AC XY:

299

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.00123

Gnomad4 AMR

AF:

0.00549

Gnomad4 ASJ

AF:

0.00923

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00415

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00615

Gnomad4 OTH

AF:

0.00992

Alfa

AF:

0.00585

Hom.:

Bravo

AF:

0.00435

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00778

AC:

ESP6500AA

AF:

0.00250

AC:

ESP6500EA

AF:

0.00814

AC:

ExAC

AF:

0.00483

AC:

586

Asia WGS

AF:

0.00144

AC:

AN:

3476

EpiCase

AF:

0.00767

EpiControl

AF:

0.00990

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.025

T;T

Eigen

Benign

-0.75

Eigen_PC

Benign

-0.60

FATHMM_MKL

Benign

0.40

LIST_S2

Benign

0.71

T;T

MetaRNN

Benign

0.0072

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.26

N;.

PrimateAI

Benign

0.22

PROVEAN

Benign

-0.43

N;N

REVEL

Benign

0.011

Sift

Benign

0.49

T;T

Sift4G

Benign

0.40

T;T

Polyphen

0.0

B;B

Vest4

0.17

MVP

0.13

MPC

0.15

ClinPred

0.0045

GERP RS

1.2

Varity_R

0.029

gMVP

0.15

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