rs10149689

Variant names:

• chr14-80949456-A-G
• rs10149689
• ENST00000555529.5:c.-172+8722T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555529.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP128	ENST00000555529.5	TSL:1	c.-172+8722T>C		intron	N/A	ENSP00000451137.1	Q86TS1
	CEP128	ENST00000556042.5	TSL:5	c.-16+8722T>C		intron	N/A	ENSP00000451214.1	G3V3F4
	CEP128	ENST00000556981.5	TSL:4	c.-268-7076T>C		intron	N/A	ENSP00000451428.1	G3V3U2

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

African (AFR) AF: 0.457 AC: 18946 AN: 41416

American (AMR) AF: 0.423 AC: 6463 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1838 AN: 3462

East Asian (EAS) AF: 0.224 AC: 1157 AN: 5158

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4814

European-Finnish (FIN) AF: 0.309 AC: 3266 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29241 AN: 67942

Other (OTH) AF: 0.449 AC: 944 AN: 2104

Alfa AF: 0.438 Hom.: 3728

Bravo AF: 0.440

Asia WGS AF: 0.394 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10149689;

hg19: chr14-81415800;