chr14-80581630-C-G

Variant names:

• chr14-80581630-C-G
• rs1868629
• NM_152446.5:c.2807-1207G>C

Variant summary

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

The NM_152446.5(CEP128):​c.2807-1207G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,938 control chromosomes in the GnomAD database, including 12,946 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 0.41 (12946 hom., cov: 32)
• Consequence: CEP128 NM_152446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP128	NM_152446.5	c.2807-1207G>C		intron_variant	Intron 19 of 24	ENST00000555265.6	NP_689659.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP128	ENST00000555265.6	c.2807-1207G>C		intron_variant	Intron 19 of 24	5	NM_152446.5	ENSP00000451162.1
CEP128	ENST00000281129.7	c.2807-1207G>C		intron_variant	Intron 18 of 23	1		ENSP00000281129.3
CEP128	ENST00000554502.5	n.1880-1207G>C		intron_variant	Intron 8 of 14	2		ENSP00000451319.1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62236 AN: 151820 Hom.: 12922 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.410 AC: 62328 AN: 151938 Hom.: 12946 Cov.: 32 AF XY: 0.410 AC XY: 30446 AN XY: 74266

African (AFR) AF: 0.466 AC: 19321 AN: 41434

American (AMR) AF: 0.354 AC: 5408 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3466

East Asian (EAS) AF: 0.522 AC: 2696 AN: 5166

South Asian (SAS) AF: 0.357 AC: 1716 AN: 4808

European-Finnish (FIN) AF: 0.449 AC: 4735 AN: 10552

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25966 AN: 67942

Other (OTH) AF: 0.393 AC: 830 AN: 2112

Alfa AF: 0.401 Hom.: 1545

Bravo AF: 0.405

Asia WGS AF: 0.448 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1868629; hg19: chr14-81047974;