rs12587252

chr14-80939578-C-T

Variant summary

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

The NM_152446.5(CEP128):c.-171-38G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 152,248 control chromosomes in the GnomAD database, including 1,411 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 0.081 (1411 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CEP128 NM_152446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP128	NM_152446.5	c.-171-38G>A		intron_variant		ENST00000555265.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP128	ENST00000555265.6	c.-171-38G>A		intron_variant		5	NM_152446.5	P2

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12295 AN: 152130 Hom.: 1399 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.00664

Gnomad FIN AF: 0.00744

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00942

Gnomad OTH AF: 0.0588

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0810 AC: 12332 AN: 152248 Hom.: 1411 Cov.: 33 AF XY: 0.0786 AC XY: 5848 AN XY: 74448

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.0393

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.00623

Gnomad4 FIN AF: 0.00744

Gnomad4 NFE AF: 0.00941

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0656 Hom.: 165

Bravo AF: 0.0896

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	6.7
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12587252; hg19: chr14-81405922;