Variant chr14-80949720-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000555529.5(CEP128):c.-172+8458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,906 control chromosomes in the GnomAD database, including 14,241 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 ( 14241 hom., cov: 32)

Consequence

CEP128
ENST00000555529.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0670

Variant links:

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]

CEP128 links:

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ACMG classification

Classification made for transcript

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 = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
CEP128	XM_011536492.3 linkuse as main transcript	c.-16+8458C>T	intron_variant
CEP128	XM_047431018.1 linkuse as main transcript	c.-268-7340C>T	intron_variant
CEP128	XM_047431019.1 linkuse as main transcript	c.-172+8458C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CEP128	ENST00000555529.5 linkuse as main transcript	c.-172+8458C>T	intron_variant	1
CEP128	ENST00000556042.5 linkuse as main transcript	c.-16+8458C>T	intron_variant	5
CEP128	ENST00000556981.5 linkuse as main transcript	c.-268-7340C>T	intron_variant	4
CEP128	ENST00000554368.1 linkuse as main transcript	n.195-3953C>T	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

64904

AN:

151788

Hom.:

14232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.458

Gnomad AMI

AF:

0.559

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.532

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.431

Gnomad OTH

AF:

0.452

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

GnomAD4 genome

AF:

0.428

AC:

64947

AN:

151906

Hom.:

14241

Cov.:

AF XY:

0.421

AC XY:

31257

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.458

Gnomad4 AMR

AF:

0.424

Gnomad4 ASJ

AF:

0.532

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.431

Gnomad4 OTH

AF:

0.449

Alfa

AF:

0.352

Hom.:

1413

Bravo

AF:

0.440

Asia WGS

AF:

0.393

AC:

1371

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

9.8

DANN

Benign

0.81

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over