10-27853365-T-TATAAATAAATAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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 (★).

• Frequency:
  • Genomes: 𝑓 0.036 (127 hom., cov: 0)
  • Exomes 𝑓: 0.013 (31 hom.)
• Consequence: ODAD2 NM_018076.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.208

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]

ACMG classification

Verdict is Benign. Variant got -10 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 criteria_provided_single_submitter, 1 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	c.3021+7259_3021+7260insTTATTTATTTAT		intron_variant		ENST00000305242.10

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0363 AC: 5370 AN: 147792 Hom.: 125 Cov.: 0

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: 89 AN: 25874 Hom.: 4 AF XY: 0.00422 AC XY: 64 AN XY: 15162

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.: 31 Cov.: 0 AF XY: 0.0146 AC XY: 1029 AN XY: 70654

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.: 0 AF XY: 0.0362 AC XY: 2601 AN XY: 71940

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: criteria provided, single submitter

Submissions by phenotype

ODAD2-related disorder Benign:1

Benign, criteria provided, single submitter

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs143299831; hg19: chr10-28142294;