Variant chr7-130393789-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018718.3(CEP41):c.*5102G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 451,426 control chromosomes in the GnomAD database, including 61,491 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22332 hom., cov: 32)

Exomes 𝑓: 0.51 ( 39159 hom. )

Consequence

CEP41
NM_018718.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.53

Variant links:

Genes affected

CEP41 (HGNC:12370): (centrosomal protein 41) This gene encodes a centrosomal and microtubule-binding protein which is predicted to have two coiled-coil domains and a rhodanese domain. In human retinal pigment epithelial cells the protein localized to centrioles and cilia. Mutations in this gene have been associated with Joubert Syndrome 15; an autosomal recessive ciliopathy and neurological disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

CEP41 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 7-130393789-C-T is Benign according to our data. Variant chr7-130393789-C-T is described in ClinVar as [Benign]. Clinvar id is 358883.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP41	NM_018718.3 linkuse as main transcript	c.*5102G>A		3_prime_UTR_variant	11/11	ENST00000223208.10

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP41	ENST00000223208.10 linkuse as main transcript	c.*5102G>A	3_prime_UTR_variant	11/11	1	NM_018718.3	P3	Q9BYV8-1
CEP41	ENST00000541543.6 linkuse as main transcript	c.*5102G>A	3_prime_UTR_variant	11/11	2
CEP41	ENST00000675649.1 linkuse as main transcript	c.*5102G>A	3_prime_UTR_variant	9/9

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81707

AN:

151922

Hom.:

22294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.631

Gnomad AMI

AF:

0.649

Gnomad AMR

AF:

0.495

Gnomad ASJ

AF:

0.551

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.510

Gnomad NFE

AF:

0.501

Gnomad OTH

AF:

0.523

GnomAD3 exomes

AF:

0.509

AC:

64518

AN:

126670

Hom.:

16516

AF XY:

0.511

AC XY:

35428

AN XY:

69354

show subpopulations

Gnomad AFR exome

AF:

0.636

Gnomad AMR exome

AF:

0.470

Gnomad ASJ exome

AF:

0.545

Gnomad EAS exome

AF:

0.492

Gnomad SAS exome

AF:

0.519

Gnomad FIN exome

AF:

0.499

Gnomad NFE exome

AF:

0.506

Gnomad OTH exome

AF:

0.521

GnomAD4 exome

AF:

0.510

AC:

152600

AN:

299386

Hom.:

39159

Cov.:

AF XY:

0.511

AC XY:

87160

AN XY:

170602

show subpopulations

Gnomad4 AFR exome

AF:

0.634

Gnomad4 AMR exome

AF:

0.472

Gnomad4 ASJ exome

AF:

0.542

Gnomad4 EAS exome

AF:

0.499

Gnomad4 SAS exome

AF:

0.521

Gnomad4 FIN exome

AF:

0.498

Gnomad4 NFE exome

AF:

0.503

Gnomad4 OTH exome

AF:

0.521

GnomAD4 genome

AF:

0.538

AC:

81805

AN:

152040

Hom.:

22332

Cov.:

AF XY:

0.535

AC XY:

39748

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.632

Gnomad4 AMR

AF:

0.496

Gnomad4 ASJ

AF:

0.551

Gnomad4 EAS

AF:

0.496

Gnomad4 SAS

AF:

0.512

Gnomad4 FIN

AF:

0.493

Gnomad4 NFE

AF:

0.501

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.508

Hom.:

22592

Bravo

AF:

0.542

Asia WGS

AF:

0.510

AC:

1771

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Joubert syndrome 15

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.0060

DANN

Benign

0.45

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