Variant chr10-27853365-T-TATAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001290021.2(ODAD2):c.1597-6_1597-3dupTTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0022 ( 4 hom., cov: 0)

Exomes 𝑓: 0.0031 ( 2 hom. )

Consequence

ODAD2
NM_001290021.2 splice_region, 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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 10-27853365-T-TATAA is Benign according to our data. Variant chr10-27853365-T-TATAA is described in ClinVar as [Benign]. Clinvar id is 3059071.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00221 (327/147954) while in subpopulation EAS AF= 0.0093 (47/5054). AF 95% confidence interval is 0.00719. There are 4 homozygotes in gnomad4. There are 177 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODAD2	NM_018076.5 linkuse as main transcript	c.3021+7256_3021+7259dupTTAT		intron_variant		ENST00000305242.10	NP_060546.2	Q5T2S8-1A0A140VKF7B7Z7Y0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODAD2	ENST00000305242.10 linkuse as main transcript	c.3021+7256_3021+7259dupTTAT		intron_variant		1	NM_018076.5	ENSP00000306410.5		Q5T2S8-1

Frequencies

GnomAD3 genomes

AF:

0.00211

AC:

312

AN:

147848

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00307

Gnomad AMI

AF:

0.00226

Gnomad AMR

AF:

0.00345

Gnomad ASJ

AF:

0.000876

Gnomad EAS

AF:

0.00928

Gnomad SAS

AF:

0.00326

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000999

Gnomad OTH

AF:

0.00198

GnomAD3 exomes

AF:

0.00483

AC:

125

AN:

25874

Hom.:

AF XY:

0.00534

AC XY:

AN XY:

15162

show subpopulations

Gnomad AFR exome

AF:

0.00151

Gnomad AMR exome

AF:

0.00275

Gnomad ASJ exome

AF:

0.00676

Gnomad EAS exome

AF:

0.00677

Gnomad SAS exome

AF:

0.00639

Gnomad FIN exome

AF:

0.00191

Gnomad NFE exome

AF:

0.00504

Gnomad OTH exome

AF:

0.00500

GnomAD4 exome

AF:

0.00308

AC:

343

AN:

111274

Hom.:

Cov.:

AF XY:

0.00335

AC XY:

233

AN XY:

69612

show subpopulations

Gnomad4 AFR exome

AF:

0.00109

Gnomad4 AMR exome

AF:

0.00275

Gnomad4 ASJ exome

AF:

0.00231

Gnomad4 EAS exome

AF:

0.00480

Gnomad4 SAS exome

AF:

0.00419

Gnomad4 FIN exome

AF:

0.00260

Gnomad4 NFE exome

AF:

0.00280

Gnomad4 OTH exome

AF:

0.00380

GnomAD4 genome

AF:

0.00221

AC:

327

AN:

147954

Hom.:

Cov.:

AF XY:

0.00246

AC XY:

177

AN XY:

71980

show subpopulations

Gnomad4 AFR

AF:

0.00343

Gnomad4 AMR

AF:

0.00344

Gnomad4 ASJ

AF:

0.000876

Gnomad4 EAS

AF:

0.00930

Gnomad4 SAS

AF:

0.00326

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000999

Gnomad4 OTH

AF:

0.00196

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

Jul 30, 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