rs12050077

Positions:

• chr14-80949720-G-A
• chr14-80949720-G-T

Variant summary

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

The ENST00000555529.5(CEP128):​c.-172+8458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,906 control chromosomes in the GnomAD database, including 14,241 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 (14241 hom., cov: 32)
• Consequence: CEP128 ENST00000555529.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP128	XM_011536492.3	c.-16+8458C>T		intron_variant
CEP128	XM_047431018.1	c.-268-7340C>T		intron_variant
CEP128	XM_047431019.1	c.-172+8458C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP128	ENST00000555529.5	c.-172+8458C>T		intron_variant		1
CEP128	ENST00000556042.5	c.-16+8458C>T		intron_variant		5
CEP128	ENST00000556981.5	c.-268-7340C>T		intron_variant		4
CEP128	ENST00000554368.1	n.195-3953C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64904 AN: 151788 Hom.: 14232 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.428 AC: 64947 AN: 151906 Hom.: 14241 Cov.: 32 AF XY: 0.421 AC XY: 31257 AN XY: 74226

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.449

Alfa AF: 0.352 Hom.: 1413

Bravo AF: 0.440

Asia WGS AF: 0.393 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12050077; hg19: chr14-81416064;