5-123349654-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001375405.1(CEP120):c.2726+290A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,904 control chromosomes in the GnomAD database, including 12,834 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.41 (12834 hom., cov: 31)
• Consequence: CEP120 NM_001375405.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0770

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 5-123349654-T-C is Benign according to our data. Variant chr5-123349654-T-C is described in ClinVar as [Benign]. Clinvar id is 1283100.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP120	NM_001375405.1	c.2726+290A>G		intron_variant		ENST00000306467.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP120	ENST00000306467.10	c.2726+290A>G		intron_variant		5	NM_001375405.1	P1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62296 AN: 151788 Hom.: 12823 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.437

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.410 AC: 62334 AN: 151904 Hom.: 12834 Cov.: 31 AF XY: 0.411 AC XY: 30501 AN XY: 74226

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.438

Alfa AF: 0.413 Hom.: 1543

Bravo AF: 0.407

Asia WGS AF: 0.481 AC: 1670 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.54

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

Other links and lift over

dbSNP: rs2115173; hg19: chr5-122685348;