Variant 14-104880295-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2

The NM_001112726.3(CEP170B):c.342G>A(p.Lys114=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0341 in 1,600,126 control chromosomes in the GnomAD database, including 1,085 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.029 ( 76 hom., cov: 33)

Exomes 𝑓: 0.035 ( 1009 hom. )

Consequence

CEP170B
NM_001112726.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.55

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=-0.45).

BP6

Variant 14-104880295-G-A is Benign according to our data. Variant chr14-104880295-G-A is described in ClinVar as [Benign]. Clinvar id is 3056165.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0286 (4350/152206) while in subpopulation SAS AF= 0.0441 (213/4832). AF 95% confidence interval is 0.0392. There are 76 homozygotes in gnomad4. There are 2158 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 76 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP170B	NM_001112726.3 linkuse as main transcript	c.342G>A	p.Lys114=	synonymous_variant	6/19	ENST00000414716.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP170B	ENST00000414716.8 linkuse as main transcript	c.342G>A	p.Lys114=	synonymous_variant	6/19	1	NM_001112726.3	P1	Q9Y4F5-2
CEP170B	ENST00000556508.5 linkuse as main transcript	c.132G>A	p.Lys44=	synonymous_variant	5/18	5			Q9Y4F5-3

Frequencies

GnomAD3 genomes

AF:

0.0286

AC:

4355

AN:

152088

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00616

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.0301

Gnomad ASJ

AF:

0.0352

Gnomad EAS

AF:

0.0336

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0319

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0388

Gnomad OTH

AF:

0.0335

GnomAD3 exomes

AF:

0.0340

AC:

7691

AN:

226382

Hom.:

155

AF XY:

0.0353

AC XY:

4345

AN XY:

123080

show subpopulations

Gnomad AFR exome

AF:

0.00559

Gnomad AMR exome

AF:

0.0235

Gnomad ASJ exome

AF:

0.0384

Gnomad EAS exome

AF:

0.0330

Gnomad SAS exome

AF:

0.0446

Gnomad FIN exome

AF:

0.0302

Gnomad NFE exome

AF:

0.0381

Gnomad OTH exome

AF:

0.0395

GnomAD4 exome

AF:

0.0347

AC:

50213

AN:

1447920

Hom.:

1009

Cov.:

AF XY:

0.0353

AC XY:

25365

AN XY:

718998

show subpopulations

Gnomad4 AFR exome

AF:

0.00550

Gnomad4 AMR exome

AF:

0.0240

Gnomad4 ASJ exome

AF:

0.0401

Gnomad4 EAS exome

AF:

0.0459

Gnomad4 SAS exome

AF:

0.0421

Gnomad4 FIN exome

AF:

0.0305

Gnomad4 NFE exome

AF:

0.0350

Gnomad4 OTH exome

AF:

0.0335

GnomAD4 genome

AF:

0.0286

AC:

4350

AN:

152206

Hom.:

Cov.:

AF XY:

0.0290

AC XY:

2158

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.00614

Gnomad4 AMR

AF:

0.0300

Gnomad4 ASJ

AF:

0.0352

Gnomad4 EAS

AF:

0.0337

Gnomad4 SAS

AF:

0.0441

Gnomad4 FIN

AF:

0.0319

Gnomad4 NFE

AF:

0.0388

Gnomad4 OTH

AF:

0.0331

Alfa

AF:

0.0337

Hom.:

Bravo

AF:

0.0273

Asia WGS

AF:

0.0350

AC:

122

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

CEP170B-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 27, 2020

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

-0.45

CADD

Benign

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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