5-123346460-T-G

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.*59A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 1,299,740 control chromosomes in the GnomAD database, including 314,436 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.69 (36018 hom., cov: 32)
  • Exomes 𝑓: 0.70 (278418 hom.)
• Consequence: CEP120 NM_001375405.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.129

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=-0.9).
• BP6: Variant 5-123346460-T-G is Benign according to our data. Variant chr5-123346460-T-G is described in ClinVar as [Benign]. Clinvar id is 1248158.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP120	NM_001375405.1	c.*59A>C		3_prime_UTR_variant	20/20	ENST00000306467.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP120	ENST00000306467.10	c.*59A>C		3_prime_UTR_variant	20/20	5	NM_001375405.1	P1

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104338 AN: 151882 Hom.: 35990 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.724

GnomAD4 exome AF: 0.695 AC: 797685 AN: 1147740 Hom.: 278418 Cov.: 14 AF XY: 0.694 AC XY: 399866 AN XY: 575848

Gnomad4 AFR exome AF: 0.646

Gnomad4 AMR exome AF: 0.645

Gnomad4 ASJ exome AF: 0.725

Gnomad4 EAS exome AF: 0.548

Gnomad4 SAS exome AF: 0.662

Gnomad4 FIN exome AF: 0.711

Gnomad4 NFE exome AF: 0.705

Gnomad4 OTH exome AF: 0.696

GnomAD4 genome AF: 0.687 AC: 104416 AN: 152000 Hom.: 36018 Cov.: 32 AF XY: 0.684 AC XY: 50819 AN XY: 74270

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.702

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: 0.726

Alfa AF: 0.705 Hom.: 44561

Bravo AF: 0.687

Asia WGS AF: 0.657 AC: 2282 AN: 3476

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 06, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.8
Dann	Benign	0.72

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: rs2303719; hg19: chr5-122682154;