14-80585009-T-A

Variant names:

• chr14-80585009-T-A
• rs17110818
• NM_152446.5:c.2807-4586A>T

Variant summary

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

The NM_152446.5(CEP128):​c.2807-4586A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,230 control chromosomes in the GnomAD database, including 2,269 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 0.16 (2269 hom., cov: 33)
• Consequence: CEP128 NM_152446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562
• Publications: 4 publications found

Genes affected

CEP128 (HGNC:20359): (centrosomal protein 128) Involved in protein localization. Located in centriole and spindle pole. Part of centriolar subdistal appendage. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP128	NM_152446.5	c.2807-4586A>T		intron_variant	Intron 19 of 24	ENST00000555265.6	NP_689659.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP128	ENST00000555265.6	c.2807-4586A>T		intron_variant	Intron 19 of 24	5	NM_152446.5	ENSP00000451162.1
CEP128	ENST00000281129.7	c.2807-4586A>T		intron_variant	Intron 18 of 23	1		ENSP00000281129.3
CEP128	ENST00000554502.5	n.1880-4586A>T		intron_variant	Intron 8 of 14	2		ENSP00000451319.1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24335 AN: 152112 Hom.: 2264 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.160 AC: 24366 AN: 152230 Hom.: 2269 Cov.: 33 AF XY: 0.163 AC XY: 12117 AN XY: 74424

African (AFR) AF: 0.110 AC: 4579 AN: 41556

American (AMR) AF: 0.110 AC: 1684 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 315 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5180

South Asian (SAS) AF: 0.0870 AC: 420 AN: 4830

European-Finnish (FIN) AF: 0.315 AC: 3338 AN: 10582

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12489 AN: 68006

Other (OTH) AF: 0.146 AC: 309 AN: 2112

Alfa AF: 0.186 Hom.: 357

Bravo AF: 0.145

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.3
DANN	Benign	0.73
PhyloP100		0.56
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: rs17110818; hg19: chr14-81051353;