rs10146516

Variant names:

• chr14-80948403-G-A
• rs10146516
• ENST00000555529.5:c.-171-8863C>T

Variant summary

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

The ENST00000555529.5(CEP128):​c.-171-8863C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,026 control chromosomes in the GnomAD database, including 14,500 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 (14500 hom., cov: 32)
• Consequence: CEP128 ENST00000555529.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 3 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=-0.96).
• 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.-171-8863C>T		intron	N/A	ENSP00000451137.1	Q86TS1
	CEP128	ENST00000556042.5	TSL:5	c.-16+9775C>T		intron	N/A	ENSP00000451214.1	G3V3F4
	CEP128	ENST00000556981.5	TSL:4	c.-268-6023C>T		intron	N/A	ENSP00000451428.1	G3V3U2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65489 AN: 151908 Hom.: 14490 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.424

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: 0.431

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.431 AC: 65534 AN: 152026 Hom.: 14500 Cov.: 32 AF XY: 0.425 AC XY: 31557 AN XY: 74316

African (AFR) AF: 0.471 AC: 19503 AN: 41446

American (AMR) AF: 0.425 AC: 6491 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1161 AN: 5184

South Asian (SAS) AF: 0.496 AC: 2391 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3264 AN: 10564

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

European-Non Finnish (NFE) AF: 0.431 AC: 29267 AN: 67952

Other (OTH) AF: 0.453 AC: 954 AN: 2104

Alfa AF: 0.432 Hom.: 1783

Bravo AF: 0.444

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	-0.96
CADD	Benign	11
DANN	Benign	0.33
PhyloP100		1.6

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: rs10146516;

hg19: chr14-81414747;