rs10146516

chr14-80948403-G-A

Variant summary

Our verdict is Benign. Variant got -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

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 = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP128	XM_011536492.3	c.-16+9775C>T		intron_variant
CEP128	XM_047431018.1	c.-268-6023C>T		intron_variant
CEP128	XM_047431019.1	c.-171-8863C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP128	ENST00000555529.5	c.-171-8863C>T		intron_variant		1
CEP128	ENST00000556042.5	c.-16+9775C>T		intron_variant		5
CEP128	ENST00000556981.5	c.-268-6023C>T		intron_variant		4
CEP128	ENST00000554368.1	n.195-2636C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.453

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	11
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10146516; hg19: chr14-81414747;