Variant chr5-123346654-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001375405.1(CEP120):c.2826T>C(p.Asp942=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 1,613,262 control chromosomes in the GnomAD database, including 399,949 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 38994 hom., cov: 31)

Exomes 𝑓: 0.70 ( 360955 hom. )

Consequence

CEP120
NM_001375405.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.325

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 5-123346654-A-G is Benign according to our data. Variant chr5-123346654-A-G is described in ClinVar as [Benign]. Clinvar id is 1167916.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.325 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP120	NM_001375405.1 linkuse as main transcript	c.2826T>C	p.Asp942=	synonymous_variant	20/20	ENST00000306467.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP120	ENST00000306467.10 linkuse as main transcript	c.2826T>C	p.Asp942=	synonymous_variant	20/20	5	NM_001375405.1	P1	Q8N960-1

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108573

AN:

151868

Hom.:

38947

Cov.:

show subpopulations

Gnomad AFR

AF:

0.749

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.736

Gnomad EAS

AF:

0.574

Gnomad SAS

AF:

0.665

Gnomad FIN

AF:

0.708

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.708

Gnomad OTH

AF:

0.746

GnomAD3 exomes

AF:

0.690

AC:

173191

AN:

250918

Hom.:

60222

AF XY:

0.692

AC XY:

93881

AN XY:

135594

show subpopulations

Gnomad AFR exome

AF:

0.754

Gnomad AMR exome

AF:

0.634

Gnomad ASJ exome

AF:

0.734

Gnomad EAS exome

AF:

0.575

Gnomad SAS exome

AF:

0.667

Gnomad FIN exome

AF:

0.711

Gnomad NFE exome

AF:

0.714

Gnomad OTH exome

AF:

0.706

GnomAD4 exome

AF:

0.702

AC:

1025252

AN:

1461276

Hom.:

360955

Cov.:

AF XY:

0.700

AC XY:

509193

AN XY:

726908

show subpopulations

Gnomad4 AFR exome

AF:

0.751

Gnomad4 AMR exome

AF:

0.646

Gnomad4 ASJ exome

AF:

0.730

Gnomad4 EAS exome

AF:

0.551

Gnomad4 SAS exome

AF:

0.668

Gnomad4 FIN exome

AF:

0.711

Gnomad4 NFE exome

AF:

0.709

Gnomad4 OTH exome

AF:

0.704

GnomAD4 genome

AF:

0.715

AC:

108678

AN:

151986

Hom.:

38994

Cov.:

AF XY:

0.712

AC XY:

52857

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.750

Gnomad4 AMR

AF:

0.712

Gnomad4 ASJ

AF:

0.736

Gnomad4 EAS

AF:

0.574

Gnomad4 SAS

AF:

0.665

Gnomad4 FIN

AF:

0.708

Gnomad4 NFE

AF:

0.708

Gnomad4 OTH

AF:

0.747

Alfa

AF:

0.714

Hom.:

75207

Bravo

AF:

0.719

Asia WGS

AF:

0.663

AC:

2304

AN:

3478

EpiCase

AF:

0.725

EpiControl

AF:

0.721

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Short-rib thoracic dysplasia 13 with or without polydactyly

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -

Joubert syndrome 31

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

4.3

DANN

Benign

0.49

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