chr1-179989674-T-C

Variant names:

• chr1-179989674-T-C
• rs2501618
• NM_014810.5:c.121-833T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014810.5(CEP350):​c.121-833T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,054 control chromosomes in the GnomAD database, including 49,997 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 0.81 (49997 hom., cov: 30)
• Consequence: CEP350 NM_014810.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 10 publications found

Genes affected

CEP350 (HGNC:24238): (centrosomal protein 350) The product of this gene is a large protein with a CAP-Gly domain typically found in cytoskeleton-associated proteins. The encoded protein primarily localizes to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. The encoded protein directly interacts with another large centrosomal protein and is required to anchor microtubules at the centrosome. It is also implicated in the regulation of a class of nuclear hormone receptors in the nucleus. Several alternatively spliced transcript variants have been found, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]

ENSG00000303101 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP350	NM_014810.5	c.121-833T>C		intron_variant	Intron 3 of 37	ENST00000367607.8	NP_055625.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP350	ENST00000367607.8	c.121-833T>C		intron_variant	Intron 3 of 37	1	NM_014810.5	ENSP00000356579.3

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122783 AN: 151936 Hom.: 49949 Cov.: 30

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.808 AC: 122886 AN: 152054 Hom.: 49997 Cov.: 30 AF XY: 0.809 AC XY: 60133 AN XY: 74336

African (AFR) AF: 0.716 AC: 29669 AN: 41448

American (AMR) AF: 0.866 AC: 13240 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2991 AN: 3472

East Asian (EAS) AF: 0.788 AC: 4074 AN: 5168

South Asian (SAS) AF: 0.865 AC: 4169 AN: 4818

European-Finnish (FIN) AF: 0.833 AC: 8797 AN: 10558

Middle Eastern (MID) AF: 0.788 AC: 230 AN: 292

European-Non Finnish (NFE) AF: 0.843 AC: 57310 AN: 67994

Other (OTH) AF: 0.805 AC: 1700 AN: 2112

Alfa AF: 0.835 Hom.: 25490

Bravo AF: 0.805

Asia WGS AF: 0.825 AC: 2871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.54
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2501618; hg19: chr1-179958809;