Variant rs1491225681 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001375405.1(CEP120):c.1431-10_1431-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 679,596 control chromosomes in the GnomAD database, including 363 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0075 ( 5 hom., cov: 12)

Exomes 𝑓: 0.078 ( 358 hom. )

Consequence

CEP120
NM_001375405.1 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: -0.159

Variant links:

Genes affected

CEP120 (HGNC:26690): (centrosomal protein 120) This gene encodes a protein that functions in the microtubule-dependent coupling of the nucleus and the centrosome. A similar protein in mouse plays a role in both interkinetic nuclear migration, which is a characteristic pattern of nuclear movement in neural progenitors, and in neural progenitor self-renewal. Mutations in this gene are predicted to result in neurogenic defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

CEP120 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 5-123386675-TTA-T is Benign according to our data. Variant chr5-123386675-TTA-T is described in ClinVar as [Benign]. Clinvar id is 476161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-123386675-TTA-T is described in Lovd as [Benign].

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP120	NM_001375405.1 linkuse as main transcript	c.1431-10_1431-9del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000306467.10	NP_001362334.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP120	ENST00000306467.10 linkuse as main transcript	c.1431-10_1431-9del		splice_polypyrimidine_tract_variant, intron_variant		5	NM_001375405.1	ENSP00000303058	P1	Q8N960-1

Frequencies

GnomAD3 genomes

AF:

0.00748

AC:

375

AN:

50158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0136

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00109

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000475

Gnomad SAS

AF:

0.00366

Gnomad FIN

AF:

0.0374

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00359

Gnomad OTH

AF:

0.00482

GnomAD3 exomes

AF:

0.0475

AC:

889

AN:

18698

Hom.:

130

AF XY:

0.0471

AC XY:

466

AN XY:

9904

show subpopulations

Gnomad AFR exome

AF:

0.0289

Gnomad AMR exome

AF:

0.0318

Gnomad ASJ exome

AF:

0.0545

Gnomad EAS exome

AF:

0.0446

Gnomad SAS exome

AF:

0.0370

Gnomad FIN exome

AF:

0.0407

Gnomad NFE exome

AF:

0.0566

Gnomad OTH exome

AF:

0.0521

GnomAD4 exome

AF:

0.0776

AC:

48839

AN:

629438

Hom.:

358

AF XY:

0.0768

AC XY:

23480

AN XY:

305718

show subpopulations

Gnomad4 AFR exome

AF:

0.0717

Gnomad4 AMR exome

AF:

0.0533

Gnomad4 ASJ exome

AF:

0.0599

Gnomad4 EAS exome

AF:

0.0715

Gnomad4 SAS exome

AF:

0.0667

Gnomad4 FIN exome

AF:

0.0655

Gnomad4 NFE exome

AF:

0.0797

Gnomad4 OTH exome

AF:

0.0747

GnomAD4 genome

AF:

0.00748

AC:

375

AN:

50158

Hom.:

Cov.:

AF XY:

0.00823

AC XY:

195

AN XY:

23696

show subpopulations

Gnomad4 AFR

AF:

0.0136

Gnomad4 AMR

AF:

0.00109

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000477

Gnomad4 SAS

AF:

0.00370

Gnomad4 FIN

AF:

0.0374

Gnomad4 NFE

AF:

0.00359

Gnomad4 OTH

AF:

0.00482

Alfa

AF:

0.00244

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

Short-rib thoracic dysplasia 13 with or without polydactyly

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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