Variant 14-104880570-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001112726.3(CEP170B):c.472+145T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 1,216,164 control chromosomes in the GnomAD database, including 249,135 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.60 ( 28318 hom., cov: 32)

Exomes 𝑓: 0.64 ( 220817 hom. )

Consequence

CEP170B
NM_001112726.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.328

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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 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.472+145T>C		intron_variant		ENST00000414716.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP170B	ENST00000414716.8 linkuse as main transcript	c.472+145T>C		intron_variant		1	NM_001112726.3	P1	Q9Y4F5-2
CEP170B	ENST00000556508.5 linkuse as main transcript	c.262+145T>C		intron_variant		5			Q9Y4F5-3

Frequencies

GnomAD3 genomes

AF:

0.603

AC:

91371

AN:

151550

Hom.:

28310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.532

Gnomad AMI

AF:

0.654

Gnomad AMR

AF:

0.589

Gnomad ASJ

AF:

0.703

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.597

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.660

Gnomad OTH

AF:

0.634

GnomAD4 exome

AF:

0.636

AC:

676967

AN:

1064496

Hom.:

220817

AF XY:

0.635

AC XY:

334100

AN XY:

525768

show subpopulations

Gnomad4 AFR exome

AF:

0.524

Gnomad4 AMR exome

AF:

0.553

Gnomad4 ASJ exome

AF:

0.700

Gnomad4 EAS exome

AF:

0.177

Gnomad4 SAS exome

AF:

0.611

Gnomad4 FIN exome

AF:

0.661

Gnomad4 NFE exome

AF:

0.661

Gnomad4 OTH exome

AF:

0.624

GnomAD4 genome

AF:

0.603

AC:

91411

AN:

151668

Hom.:

28318

Cov.:

AF XY:

0.600

AC XY:

44489

AN XY:

74106

show subpopulations

Gnomad4 AFR

AF:

0.531

Gnomad4 AMR

AF:

0.588

Gnomad4 ASJ

AF:

0.703

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.598

Gnomad4 FIN

AF:

0.673

Gnomad4 NFE

AF:

0.660

Gnomad4 OTH

AF:

0.631

Alfa

AF:

0.622

Hom.:

3541

Bravo

AF:

0.592

Asia WGS

AF:

0.413

AC:

1442

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.18

DANN

Benign

0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.97

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over