rs17110818

chr14-80585009-T-Achr14-80585009-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

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 = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP128	NM_152446.5	c.2807-4586A>T		intron_variant		ENST00000555265.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP128	ENST00000555265.6	c.2807-4586A>T		intron_variant		5	NM_152446.5	P2
CEP128	ENST00000281129.7	c.2807-4586A>T		intron_variant		1		P2
CEP128	ENST00000554502.5	c.1882-4586A>T		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.146

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

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: rs17110818; hg19: chr14-81051353;