Variant chr14-104878486-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001112726.3(CEP170B):c.318G>A(p.Pro106=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 1,611,574 control chromosomes in the GnomAD database, including 1,106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.029 ( 78 hom., cov: 33)

Exomes 𝑓: 0.035 ( 1028 hom. )

Consequence

CEP170B
NM_001112726.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.63

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 14-104878486-G-A is Benign according to our data. Variant chr14-104878486-G-A is described in ClinVar as [Benign]. Clinvar id is 3055708.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.63 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0288 (4390/152328) while in subpopulation SAS AF= 0.0434 (209/4820). AF 95% confidence interval is 0.0385. There are 78 homozygotes in gnomad4. There are 2174 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 78 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP170B	NM_001112726.3 linkuse as main transcript	c.318G>A	p.Pro106=	synonymous_variant	5/19	ENST00000414716.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP170B	ENST00000414716.8 linkuse as main transcript	c.318G>A	p.Pro106=	synonymous_variant	5/19	1	NM_001112726.3	P1	Q9Y4F5-2
CEP170B	ENST00000556508.5 linkuse as main transcript	c.108G>A	p.Pro36=	synonymous_variant	4/18	5			Q9Y4F5-3

Frequencies

GnomAD3 genomes

AF:

0.0289

AC:

4395

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00635

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.0311

Gnomad ASJ

AF:

0.0372

Gnomad EAS

AF:

0.0341

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.0320

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0389

Gnomad OTH

AF:

0.0339

GnomAD3 exomes

AF:

0.0345

AC:

8516

AN:

246920

Hom.:

174

AF XY:

0.0360

AC XY:

4833

AN XY:

134426

show subpopulations

Gnomad AFR exome

AF:

0.00578

Gnomad AMR exome

AF:

0.0243

Gnomad ASJ exome

AF:

0.0411

Gnomad EAS exome

AF:

0.0335

Gnomad SAS exome

AF:

0.0449

Gnomad FIN exome

AF:

0.0304

Gnomad NFE exome

AF:

0.0388

Gnomad OTH exome

AF:

0.0399

GnomAD4 exome

AF:

0.0349

AC:

50939

AN:

1459246

Hom.:

1028

Cov.:

AF XY:

0.0355

AC XY:

25795

AN XY:

725942

show subpopulations

Gnomad4 AFR exome

AF:

0.00553

Gnomad4 AMR exome

AF:

0.0247

Gnomad4 ASJ exome

AF:

0.0420

Gnomad4 EAS exome

AF:

0.0465

Gnomad4 SAS exome

AF:

0.0422

Gnomad4 FIN exome

AF:

0.0303

Gnomad4 NFE exome

AF:

0.0352

Gnomad4 OTH exome

AF:

0.0342

GnomAD4 genome

AF:

0.0288

AC:

4390

AN:

152328

Hom.:

Cov.:

AF XY:

0.0292

AC XY:

2174

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00633

Gnomad4 AMR

AF:

0.0310

Gnomad4 ASJ

AF:

0.0372

Gnomad4 EAS

AF:

0.0341

Gnomad4 SAS

AF:

0.0434

Gnomad4 FIN

AF:

0.0320

Gnomad4 NFE

AF:

0.0389

Gnomad4 OTH

AF:

0.0336

Alfa

AF:

0.0325

Hom.:

Bravo

AF:

0.0278

Asia WGS

AF:

0.0350

AC:

123

AN:

3478

EpiCase

AF:

0.0424

EpiControl

AF:

0.0439

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

-0.67

CADD

Benign

1.5

DANN

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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