Variant 10-27853365-T-TATAAATAAATAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_018076.5(ODAD2):c.3021+7259_3021+7260insTTATTTATTTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.036 ( 127 hom., cov: 0)

Exomes 𝑓: 0.013 ( 31 hom. )

Consequence

ODAD2
NM_018076.5 intron

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.208

Variant links:

Genes affected

ODAD2 (HGNC:25583): (outer dynein arm docking complex subunit 2) The protein encoded by this gene contains ten Armadillo repeat motifs (ARMs) and one HEAT repeat, and is thought to be involved in ciliary and flagellar movement. This protein has been shown to localize to the ciliary axonemes and at the ciliary base of respiratory cells. Studies indicate that mutations in this gene cause partial outer dynein arm (ODA) defects in respiratory cilia. The cilia of cells with mutations in this gene displayed either reduced ciliary beat frequency and amplitude, or, complete immotility. Some individuals with primary ciliary dyskensia (PCD) have been shown to have mutations in this gene. PCD is characterized by chronic airway disease and left/right body asymmetry defects. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

ODAD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 10-27853365-T-TATAAATAAATAA is Benign according to our data. Variant chr10-27853365-T-TATAAATAAATAA is described in ClinVar as [Benign]. Clinvar id is 3039546.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODAD2	NM_018076.5 linkuse as main transcript	c.3021+7259_3021+7260insTTATTTATTTAT		intron_variant		ENST00000305242.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD2	ENST00000305242.10 linkuse as main transcript	c.3021+7259_3021+7260insTTATTTATTTAT		intron_variant		1	NM_018076.5	P1	Q5T2S8-1

Frequencies

GnomAD3 genomes

AF:

0.0363

AC:

5370

AN:

147792

Hom.:

125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0604

Gnomad AMI

AF:

0.0633

Gnomad AMR

AF:

0.0419

Gnomad ASJ

AF:

0.0158

Gnomad EAS

AF:

0.0489

Gnomad SAS

AF:

0.0219

Gnomad FIN

AF:

0.0113

Gnomad MID

AF:

0.0133

Gnomad NFE

AF:

0.0255

Gnomad OTH

AF:

0.0252

GnomAD3 exomes

AF:

0.00344

AC:

AN:

25874

Hom.:

AF XY:

0.00422

AC XY:

AN XY:

15162

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00157

Gnomad ASJ exome

AF:

0.00208

Gnomad EAS exome

AF:

0.00554

Gnomad SAS exome

AF:

0.00383

Gnomad FIN exome

AF:

0.00191

Gnomad NFE exome

AF:

0.00459

Gnomad OTH exome

AF:

0.00500

GnomAD4 exome

AF:

0.0125

AC:

1414

AN:

112708

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

1029

AN XY:

70654

show subpopulations

Gnomad4 AFR exome

AF:

0.0245

Gnomad4 AMR exome

AF:

0.00428

Gnomad4 ASJ exome

AF:

0.00638

Gnomad4 EAS exome

AF:

0.0368

Gnomad4 SAS exome

AF:

0.00655

Gnomad4 FIN exome

AF:

0.00492

Gnomad4 NFE exome

AF:

0.0150

Gnomad4 OTH exome

AF:

0.0151

GnomAD4 genome

AF:

0.0364

AC:

5381

AN:

147898

Hom.:

127

Cov.:

AF XY:

0.0362

AC XY:

2601

AN XY:

71940

show subpopulations

Gnomad4 AFR

AF:

0.0605

Gnomad4 AMR

AF:

0.0417

Gnomad4 ASJ

AF:

0.0158

Gnomad4 EAS

AF:

0.0489

Gnomad4 SAS

AF:

0.0222

Gnomad4 FIN

AF:

0.0113

Gnomad4 NFE

AF:

0.0255

Gnomad4 OTH

AF:

0.0250

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ODAD2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 08, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over