Variant chr14-104877956-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_001112726.3(CEP170B):c.267C>T(p.Phe89=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 1,603,718 control chromosomes in the GnomAD database, including 239,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.45 ( 17180 hom., cov: 29)

Exomes 𝑓: 0.54 ( 221906 hom. )

Consequence

CEP170B
NM_001112726.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.743

Variant links:

Genes affected

CEP170B (HGNC:20362): (centrosomal protein 170B) Predicted to be located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

CEP170B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP6

Variant 14-104877956-C-T is Benign according to our data. Variant chr14-104877956-C-T is described in ClinVar as [Benign]. Clinvar id is 3058985.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.743 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP170B	NM_001112726.3 linkuse as main transcript	c.267C>T	p.Phe89=	synonymous_variant	4/19	ENST00000414716.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP170B	ENST00000414716.8 linkuse as main transcript	c.267C>T	p.Phe89=	synonymous_variant	4/19	1	NM_001112726.3	P1	Q9Y4F5-2
CEP170B	ENST00000556508.5 linkuse as main transcript	c.57C>T	p.Phe19=	synonymous_variant	3/18	5			Q9Y4F5-3

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67281

AN:

151036

Hom.:

17180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.553

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.653

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.558

Gnomad MID

AF:

0.679

Gnomad NFE

AF:

0.564

Gnomad OTH

AF:

0.498

GnomAD3 exomes

AF:

0.500

AC:

119315

AN:

238788

Hom.:

31627

AF XY:

0.510

AC XY:

66194

AN XY:

129780

show subpopulations

Gnomad AFR exome

AF:

0.203

Gnomad AMR exome

AF:

0.474

Gnomad ASJ exome

AF:

0.657

Gnomad EAS exome

AF:

0.174

Gnomad SAS exome

AF:

0.499

Gnomad FIN exome

AF:

0.560

Gnomad NFE exome

AF:

0.572

Gnomad OTH exome

AF:

0.541

GnomAD4 exome

AF:

0.544

AC:

790430

AN:

1452564

Hom.:

221906

Cov.:

AF XY:

0.544

AC XY:

392756

AN XY:

721976

show subpopulations

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.481

Gnomad4 ASJ exome

AF:

0.649

Gnomad4 EAS exome

AF:

0.131

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.556

Gnomad4 NFE exome

AF:

0.573

Gnomad4 OTH exome

AF:

0.530

GnomAD4 genome

AF:

0.445

AC:

67289

AN:

151154

Hom.:

17180

Cov.:

AF XY:

0.445

AC XY:

32856

AN XY:

73846

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.498

Gnomad4 ASJ

AF:

0.653

Gnomad4 EAS

AF:

0.184

Gnomad4 SAS

AF:

0.484

Gnomad4 FIN

AF:

0.558

Gnomad4 NFE

AF:

0.564

Gnomad4 OTH

AF:

0.497

Alfa

AF:

0.528

Hom.:

11313

Bravo

AF:

0.431

Asia WGS

AF:

0.327

AC:

1140

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CEP170B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

4.7

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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