Variant chr11-101948072-C-G 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_020802.4(CEP126):c.436C>G(p.Gln146Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 1,611,840 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0014 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0021 ( 19 hom. )

Consequence

CEP126
NM_020802.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.30

Variant links:

Genes affected

CEP126 (HGNC:29264): (centrosomal protein 126) Involved in cilium assembly; cytoplasmic microtubule organization; and mitotic spindle organization. Located in centrosome; ciliary base; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

CEP126 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=0.007989496).

BP6

Variant 11-101948072-C-G is Benign according to our data. Variant chr11-101948072-C-G is described in ClinVar as [Benign]. Clinvar id is 774477.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP126	NM_020802.4 link	c.436C>G	p.Gln146Glu	missense_variant	4/11	ENST00000263468.13	NP_065853.3	Q9P2H0
CEP126	NM_001363543.2 link	c.-844C>G		5_prime_UTR_variant	4/12		NP_001350472.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CEP126	ENST00000263468.13 link	c.436C>G	p.Gln146Glu	missense_variant	4/11	1	NM_020802.4	ENSP00000263468.8	Q9P2H0
CEP126	ENST00000532529.1 link	n.76C>G		non_coding_transcript_exon_variant	2/10	5		ENSP00000433643.1	H0YDI0
CEP126	ENST00000670091.1 link	n.436C>G		non_coding_transcript_exon_variant	4/12			ENSP00000499679.1	A0A590UK33
CEP126	ENST00000670318.1 link	n.436C>G		non_coding_transcript_exon_variant	4/12			ENSP00000499404.1	A0A590UJH0

Frequencies

GnomAD3 genomes

AF:

0.00142

AC:

216

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00137

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0122

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00154

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00267

AC:

671

AN:

251002

Hom.:

AF XY:

0.00330

AC XY:

448

AN XY:

135658

show subpopulations

Gnomad AFR exome

AF:

0.000370

Gnomad AMR exome

AF:

0.00110

Gnomad ASJ exome

AF:

0.00149

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0123

Gnomad FIN exome

AF:

0.000324

Gnomad NFE exome

AF:

0.00193

Gnomad OTH exome

AF:

0.00131

GnomAD4 exome

AF:

0.00208

AC:

3031

AN:

1459602

Hom.:

Cov.:

AF XY:

0.00240

AC XY:

1746

AN XY:

726136

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.00134

Gnomad4 ASJ exome

AF:

0.00123

Gnomad4 EAS exome

AF:

0.0000758

Gnomad4 SAS exome

AF:

0.0116

Gnomad4 FIN exome

AF:

0.000506

Gnomad4 NFE exome

AF:

0.00153

Gnomad4 OTH exome

AF:

0.00250

GnomAD4 genome

AF:

0.00141

AC:

215

AN:

152238

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0120

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00154

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00157

Hom.:

Bravo

AF:

0.00115

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00116

AC:

ExAC

AF:

0.00299

AC:

363

Asia WGS

AF:

0.00376

AC:

AN:

3474

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 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.29

CADD

Uncertain

DANN

Uncertain

0.99

Eigen

Uncertain

0.68

Eigen_PC

Uncertain

0.65

FATHMM_MKL

Uncertain

0.87

MetaRNN

Benign

0.0080

MetaSVM

Benign

-1.1

PrimateAI

Benign

0.40

PROVEAN

Benign

-2.3

REVEL

Benign

0.20

Sift

Uncertain

0.0080

Sift4G

Pathogenic

0.0

Vest4

0.44

MVP

0.51

MPC

0.56

ClinPred

0.034

GERP RS

5.4

gMVP

0.20

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