chr14-80949456-A-G

Variant names:

• chr14-80949456-A-G
• rs10149689
• ENST00000555529.5:c.-172+8722T>C

Variant summary

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

The ENST00000555529.5(CEP128):​c.-172+8722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,932 control chromosomes in the GnomAD database, including 14,230 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 (14230 hom., cov: 31)
• Consequence: CEP128 ENST00000555529.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 10 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=-0.92).
• 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 rank	MANE	Protein	UniProt
CEP128	XM_011536492.3	c.-16+8722T>C		intron_variant	Intron 2 of 25		XP_011534794.1
CEP128	XM_047431018.1	c.-268-7076T>C		intron_variant	Intron 2 of 26		XP_047286974.1
CEP128	XM_047431019.1	c.-172+8722T>C		intron_variant	Intron 2 of 25		XP_047286975.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP128	ENST00000555529.5	c.-172+8722T>C		intron_variant	Intron 2 of 7	1		ENSP00000451137.1
CEP128	ENST00000556042.5	c.-16+8722T>C		intron_variant	Intron 2 of 5	5		ENSP00000451214.1
CEP128	ENST00000556981.5	c.-268-7076T>C		intron_variant	Intron 2 of 4	4		ENSP00000451428.1
CEP128	ENST00000554368.1	n.195-3689T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64861 AN: 151814 Hom.: 14221 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.423

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: 0.430

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.427 AC: 64904 AN: 151932 Hom.: 14230 Cov.: 31 AF XY: 0.421 AC XY: 31241 AN XY: 74254

African (AFR) AF: 0.457 AC: 18946 AN: 41416

American (AMR) AF: 0.423 AC: 6463 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1838 AN: 3462

East Asian (EAS) AF: 0.224 AC: 1157 AN: 5158

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4814

European-Finnish (FIN) AF: 0.309 AC: 3266 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29241 AN: 67942

Other (OTH) AF: 0.449 AC: 944 AN: 2104

Alfa AF: 0.438 Hom.: 3728

Bravo AF: 0.440

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	-0.92
CADD	Benign	4.2
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10149689; hg19: chr14-81415800;