Variant rs2028414 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001112726.3(CEP170B):c.594A>C(p.Pro198=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 1,529,066 control chromosomes in the GnomAD database, including 306,830 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.59 ( 27392 hom., cov: 27)

Exomes 𝑓: 0.63 ( 279438 hom. )

Consequence

CEP170B
NM_001112726.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.83

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 14-104883051-A-C is Benign according to our data. Variant chr14-104883051-A-C is described in ClinVar as [Benign]. Clinvar id is 3058875.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.84 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 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.594A>C	p.Pro198=	synonymous_variant	8/19	ENST00000414716.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP170B	ENST00000414716.8 linkuse as main transcript	c.594A>C	p.Pro198=	synonymous_variant	8/19	1	NM_001112726.3	P1	Q9Y4F5-2
CEP170B	ENST00000556508.5 linkuse as main transcript	c.384A>C	p.Pro128=	synonymous_variant	7/18	5			Q9Y4F5-3

Frequencies

GnomAD3 genomes

AF:

0.593

AC:

89474

AN:

150994

Hom.:

27392

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.704

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.667

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.652

Gnomad OTH

AF:

0.626

GnomAD3 exomes

AF:

0.578

AC:

84752

AN:

146532

Hom.:

25823

AF XY:

0.586

AC XY:

47002

AN XY:

80140

show subpopulations

Gnomad AFR exome

AF:

0.498

Gnomad AMR exome

AF:

0.527

Gnomad ASJ exome

AF:

0.703

Gnomad EAS exome

AF:

0.202

Gnomad SAS exome

AF:

0.623

Gnomad FIN exome

AF:

0.663

Gnomad NFE exome

AF:

0.641

Gnomad OTH exome

AF:

0.610

GnomAD4 exome

AF:

0.631

AC:

869874

AN:

1377952

Hom.:

279438

Cov.:

AF XY:

0.631

AC XY:

428088

AN XY:

678104

show subpopulations

Gnomad4 AFR exome

AF:

0.505

Gnomad4 AMR exome

AF:

0.542

Gnomad4 ASJ exome

AF:

0.700

Gnomad4 EAS exome

AF:

0.176

Gnomad4 SAS exome

AF:

0.620

Gnomad4 FIN exome

AF:

0.658

Gnomad4 NFE exome

AF:

0.652

Gnomad4 OTH exome

AF:

0.620

GnomAD4 genome

AF:

0.592

AC:

89504

AN:

151114

Hom.:

27392

Cov.:

AF XY:

0.590

AC XY:

43557

AN XY:

73772

show subpopulations

Gnomad4 AFR

AF:

0.509

Gnomad4 AMR

AF:

0.585

Gnomad4 ASJ

AF:

0.704

Gnomad4 EAS

AF:

0.219

Gnomad4 SAS

AF:

0.613

Gnomad4 FIN

AF:

0.667

Gnomad4 NFE

AF:

0.652

Gnomad4 OTH

AF:

0.623

Alfa

AF:

0.640

Hom.:

38578

Bravo

AF:

0.582

Asia WGS

AF:

0.413

AC:

1440

AN:

3476

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

-0.99

CADD

Benign

0.44

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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