Variant 19-32879255-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_032816.5(CEP89):c.2259T>G(p.Val753=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 1,613,506 control chromosomes in the GnomAD database, including 89,618 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 5534 hom., cov: 33)

Exomes 𝑓: 0.33 ( 84084 hom. )

Consequence

CEP89
NM_032816.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.716

Variant links:

Genes affected

CEP89 (HGNC:25907): (centrosomal protein 89) Involved in non-motile cilium assembly. Acts upstream of or within cilium assembly. Located in several cellular components, including cytosol; microtubule cytoskeleton; and non-motile cilium. Part of ciliary transition fiber. [provided by Alliance of Genome Resources, Apr 2022]

CEP89 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 19-32879255-A-C is Benign according to our data. Variant chr19-32879255-A-C is described in ClinVar as [Benign]. Clinvar id is 1599009.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.716 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CEP89	NM_032816.5 linkuse as main transcript	c.2259T>G	p.Val753=	synonymous_variant	19/19	ENST00000305768.10
CEP89	XM_005259344.4 linkuse as main transcript	c.2187T>G	p.Val729=	synonymous_variant	19/19
CEP89	XM_047439562.1 linkuse as main transcript	c.1518T>G	p.Val506=	synonymous_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP89	ENST00000305768.10 linkuse as main transcript	c.2259T>G	p.Val753=	synonymous_variant	19/19	1	NM_032816.5	P3	Q96ST8-1
CEP89	ENST00000586984.6 linkuse as main transcript	c.*868T>G		3_prime_UTR_variant, NMD_transcript_variant	18/18	1
CEP89	ENST00000591698.5 linkuse as main transcript	c.*1593T>G		3_prime_UTR_variant, NMD_transcript_variant	18/18	2

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37631

AN:

152100

Hom.:

5537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.306

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.288

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.243

GnomAD3 exomes

AF:

0.261

AC:

65690

AN:

251424

Hom.:

9839

AF XY:

0.268

AC XY:

36460

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.0982

Gnomad AMR exome

AF:

0.133

Gnomad ASJ exome

AF:

0.289

Gnomad EAS exome

AF:

0.118

Gnomad SAS exome

AF:

0.205

Gnomad FIN exome

AF:

0.305

Gnomad NFE exome

AF:

0.350

Gnomad OTH exome

AF:

0.288

GnomAD4 exome

AF:

0.329

AC:

480818

AN:

1461288

Hom.:

84084

Cov.:

AF XY:

0.326

AC XY:

237048

AN XY:

726972

show subpopulations

Gnomad4 AFR exome

AF:

0.0933

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.289

Gnomad4 EAS exome

AF:

0.0929

Gnomad4 SAS exome

AF:

0.210

Gnomad4 FIN exome

AF:

0.307

Gnomad4 NFE exome

AF:

0.365

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.247

AC:

37627

AN:

152218

Hom.:

5534

Cov.:

AF XY:

0.241

AC XY:

17953

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.288

Gnomad4 EAS

AF:

0.109

Gnomad4 SAS

AF:

0.211

Gnomad4 FIN

AF:

0.286

Gnomad4 NFE

AF:

0.352

Gnomad4 OTH

AF:

0.240

Alfa

AF:

0.320

Hom.:

5127

Bravo

AF:

0.234

Asia WGS

AF:

0.132

AC:

458

AN:

3478

EpiCase

AF:

0.343

EpiControl

AF:

0.344

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.9

DANN

Benign

0.44

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over