Variant chr1-243136134-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014812.3(CEP170):c.4319+9A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0992 in 1,450,766 control chromosomes in the GnomAD database, including 2,232 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 243 hom., cov: 32)

Exomes 𝑓: 0.10 ( 1989 hom. )

Consequence

CEP170
NM_014812.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.385

Variant links:

Genes affected

CEP170 (HGNC:28920): (centrosomal protein 170) The product of this gene is a component of the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. During interphase, the encoded protein localizes to the sub-distal appendages of mature centrioles, which are microtubule-based structures thought to help organize centrosomes. During mitosis, the protein associates with spindle microtubules near the centrosomes. The protein interacts with and is phosphorylated by polo-like kinase 1, and functions in maintaining microtubule organization and cell morphology. The human genome contains a putative transcribed pseudogene. Several alternatively spliced transcript variants of this gene have been found, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]

CEP170 links:

CEP170 (HGNC:):

CEP170 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-243136134-T-A is Benign according to our data. Variant chr1-243136134-T-A is described in ClinVar as [Benign]. Clinvar id is 770336.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP170	NM_014812.3 linkuse as main transcript	c.4319+9A>T		intron_variant		ENST00000366542.6	NP_055627.2	Q5SW79-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CEP170	ENST00000366542.6 linkuse as main transcript	c.4319+9A>T	intron_variant	5	NM_014812.3	ENSP00000355500.1	Q5SW79-1
CEP170	ENST00000366544.5 linkuse as main transcript	c.4025+9A>T	intron_variant	5		ENSP00000355502.1	Q5SW79-3
CEP170	ENST00000366543.5 linkuse as main transcript	c.3947+9A>T	intron_variant	5		ENSP00000355501.1	Q5SW79-2

Frequencies

GnomAD3 genomes

AF:

0.0847

AC:

12852

AN:

151660

Hom.:

243

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0220

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.0965

Gnomad ASJ

AF:

0.0719

Gnomad EAS

AF:

0.0621

Gnomad SAS

AF:

0.0940

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.0478

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.0779

GnomAD3 exomes

AF:

0.0976

AC:

11439

AN:

117160

Hom.:

187

AF XY:

0.0979

AC XY:

6049

AN XY:

61800

show subpopulations

Gnomad AFR exome

AF:

0.0206

Gnomad AMR exome

AF:

0.111

Gnomad ASJ exome

AF:

0.0652

Gnomad EAS exome

AF:

0.0584

Gnomad SAS exome

AF:

0.0951

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.112

Gnomad OTH exome

AF:

0.108

GnomAD4 exome

AF:

0.101

AC:

131043

AN:

1298988

Hom.:

1989

Cov.:

AF XY:

0.101

AC XY:

64782

AN XY:

643636

show subpopulations

Gnomad4 AFR exome

AF:

0.0158

Gnomad4 AMR exome

AF:

0.112

Gnomad4 ASJ exome

AF:

0.0667

Gnomad4 EAS exome

AF:

0.0453

Gnomad4 SAS exome

AF:

0.0878

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.107

Gnomad4 OTH exome

AF:

0.0881

GnomAD4 genome

AF:

0.0846

AC:

12846

AN:

151778

Hom.:

243

Cov.:

AF XY:

0.0847

AC XY:

6287

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.0219

Gnomad4 AMR

AF:

0.0963

Gnomad4 ASJ

AF:

0.0719

Gnomad4 EAS

AF:

0.0621

Gnomad4 SAS

AF:

0.0947

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.117

Gnomad4 OTH

AF:

0.0766

Alfa

AF:

0.0606

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 30, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.8

DANN

Benign

0.69

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