rs10149689

Positions:

• chr14-80949456-A-G

Variant summary

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

The ENST00000555529.5(CEP128):​c.-172+8722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,932 control chromosomes in the GnomAD database, including 14,230 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 0.43 (14230 hom., cov: 31)
• Consequence: CEP128 ENST00000555529.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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]

CEP128 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP128	XM_011536492.3	c.-16+8722T>C		intron_variant			XP_011534794.1
CEP128	XM_047431018.1	c.-268-7076T>C		intron_variant			XP_047286974.1
CEP128	XM_047431019.1	c.-172+8722T>C		intron_variant			XP_047286975.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP128	ENST00000555529.5	c.-172+8722T>C		intron_variant		1		ENSP00000451137.1
CEP128	ENST00000556042.5	c.-16+8722T>C		intron_variant		5		ENSP00000451214.1
CEP128	ENST00000556981.5	c.-268-7076T>C		intron_variant		4		ENSP00000451428.1
CEP128	ENST00000554368.1	n.195-3689T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64861 AN: 151814 Hom.: 14221 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.427 AC: 64904 AN: 151932 Hom.: 14230 Cov.: 31 AF XY: 0.421 AC XY: 31241 AN XY: 74254

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.449

Alfa AF: 0.437 Hom.: 3635

Bravo AF: 0.440

Asia WGS AF: 0.394 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10149689; hg19: chr14-81415800;