rs5810000

chr14-80617101-GA-Gchr14-80617101-GA-GAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_152446.5(CEP128):c.2807-36679del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,522 control chromosomes in the GnomAD database, including 7,345 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7345 hom., cov: 0)
• Consequence: CEP128 NM_152446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP128	NM_152446.5	c.2807-36679del		intron_variant		ENST00000555265.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP128	ENST00000555265.6	c.2807-36679del		intron_variant		5	NM_152446.5	P2
CEP128	ENST00000281129.7	c.2807-36679del		intron_variant		1		P2
CEP128	ENST00000554502.5	c.1882-36679del		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45931 AN: 151410 Hom.: 7334 Cov.: 0

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.303 AC: 45974 AN: 151522 Hom.: 7345 Cov.: 0 AF XY: 0.301 AC XY: 22278 AN XY: 74000

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.309

Alfa AF: 0.279 Hom.: 739

Bravo AF: 0.311

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5810000; hg19: chr14-81083445;