rs3808909

Positions:

• chr10-27987344-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_018076.5(ODAD2):​c.382+42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,578,882 control chromosomes in the GnomAD database, including 46,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3500 hom., cov: 32)
  • Exomes 𝑓: 0.24 (42659 hom.)
• Consequence: ODAD2 NM_018076.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.31

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 10-27987344-G-A is Benign according to our data. Variant chr10-27987344-G-A is described in ClinVar as [Benign]. Clinvar id is 1235317.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODAD2	NM_018076.5	c.382+42C>T		intron_variant		ENST00000305242.10	NP_060546.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODAD2	ENST00000305242.10	c.382+42C>T		intron_variant		1	NM_018076.5	ENSP00000306410.5
ODAD2	ENST00000673439.1	c.382+42C>T		intron_variant				ENSP00000500782.1
ODAD2	ENST00000434029.1	n.64+42C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30334 AN: 151964 Hom.: 3498 Cov.: 32

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.213

GnomAD3 exomes AF: 0.222 AC: 52818 AN: 237868 Hom.: 6302 AF XY: 0.225 AC XY: 28946 AN XY: 128510

Gnomad AFR exome AF: 0.0994

Gnomad AMR exome AF: 0.262

Gnomad ASJ exome AF: 0.201

Gnomad EAS exome AF: 0.0530

Gnomad SAS exome AF: 0.201

Gnomad FIN exome AF: 0.288

Gnomad NFE exome AF: 0.250

Gnomad OTH exome AF: 0.237

GnomAD4 exome AF: 0.240 AC: 341836 AN: 1426800 Hom.: 42659 Cov.: 26 AF XY: 0.239 AC XY: 169402 AN XY: 707956

Gnomad4 AFR exome AF: 0.0962

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.192

Gnomad4 EAS exome AF: 0.0617

Gnomad4 SAS exome AF: 0.208

Gnomad4 FIN exome AF: 0.282

Gnomad4 NFE exome AF: 0.252

Gnomad4 OTH exome AF: 0.222

GnomAD4 genome AF: 0.199 AC: 30332 AN: 152082 Hom.: 3500 Cov.: 32 AF XY: 0.201 AC XY: 14973 AN XY: 74316

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0578

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.211

Alfa AF: 0.222 Hom.: 1075

Bravo AF: 0.193

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.35
DANN	Benign	0.36

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

Other links and lift over

dbSNP: rs3808909; hg19: chr10-28276273;