chr14-80939578-C-T

Variant names:

• chr14-80939578-C-T
• rs12587252
• NM_152446.5:c.-171-38G>A

Variant summary

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

The NM_152446.5(CEP128):​c.-171-38G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 152,248 control chromosomes in the GnomAD database, including 1,411 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 0.081 (1411 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CEP128 NM_152446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 5 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP128	NM_152446.5	c.-171-38G>A		intron_variant	Intron 1 of 24	ENST00000555265.6	NP_689659.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP128	ENST00000555265.6	c.-171-38G>A		intron_variant	Intron 1 of 24	5	NM_152446.5	ENSP00000451162.1

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12295 AN: 152130 Hom.: 1399 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.00664

Gnomad FIN AF: 0.00744

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00942

Gnomad OTH AF: 0.0588

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0810 AC: 12332 AN: 152248 Hom.: 1411 Cov.: 33 AF XY: 0.0786 AC XY: 5848 AN XY: 74448

African (AFR) AF: 0.256 AC: 10642 AN: 41502

American (AMR) AF: 0.0393 AC: 602 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3470

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5188

South Asian (SAS) AF: 0.00623 AC: 30 AN: 4818

European-Finnish (FIN) AF: 0.00744 AC: 79 AN: 10624

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.00941 AC: 640 AN: 68026

Other (OTH) AF: 0.0582 AC: 123 AN: 2114

Alfa AF: 0.0448 Hom.: 1139

Bravo AF: 0.0896

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.7
DANN	Benign	0.78
PhyloP100		-0.084
PromoterAI		-0.0092	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12587252; hg19: chr14-81405922;