rs1047440

Positions:

• chr5-123346140-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375405.1(CEP120):​c.*379G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 169,566 control chromosomes in the GnomAD database, including 14,120 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.41 (12561 hom., cov: 32)
  • Exomes 𝑓: 0.40 (1559 hom.)
• Consequence: CEP120 NM_001375405.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP120	NM_001375405.1	c.*379G>A		3_prime_UTR_variant	20/20	ENST00000306467.10	NP_001362334.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP120	ENST00000306467.10	c.*379G>A		3_prime_UTR_variant	20/20	5	NM_001375405.1	ENSP00000303058	P1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61552 AN: 151814 Hom.: 12556 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.432

GnomAD4 exome AF: 0.403 AC: 7108 AN: 17634 Hom.: 1559 Cov.: 0 AF XY: 0.402 AC XY: 3657 AN XY: 9100

Gnomad4 AFR exome AF: 0.315

Gnomad4 AMR exome AF: 0.401

Gnomad4 ASJ exome AF: 0.312

Gnomad4 EAS exome AF: 0.437

Gnomad4 SAS exome AF: 0.423

Gnomad4 FIN exome AF: 0.411

Gnomad4 NFE exome AF: 0.406

Gnomad4 OTH exome AF: 0.390

GnomAD4 genome AF: 0.405 AC: 61579 AN: 151932 Hom.: 12561 Cov.: 32 AF XY: 0.406 AC XY: 30158 AN XY: 74224

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.433

Alfa AF: 0.427 Hom.: 22099

Bravo AF: 0.400

Asia WGS AF: 0.470 AC: 1631 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.97
DANN	Benign	0.82

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: rs1047440; hg19: chr5-122681834;