10-27812184-CTT-C

Variant summary

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

The NM_018076.5(ODAD2):c.*326_*327del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 280,656 control chromosomes in the GnomAD database, including 77,131 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.69 (37526 hom., cov: 0)
  • Exomes 𝑓: 0.78 (39605 hom.)
• Consequence: ODAD2 NM_018076.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

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 10-27812184-CTT-C is Benign according to our data. Variant chr10-27812184-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1264953.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODAD2	NM_018076.5	c.*326_*327del		3_prime_UTR_variant	20/20	ENST00000305242.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD2	ENST00000305242.10	c.*326_*327del		3_prime_UTR_variant	20/20	1	NM_018076.5	P1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104097 AN: 151708 Hom.: 37520 Cov.: 0

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.711

GnomAD4 exome AF: 0.778 AC: 100200 AN: 128830 Hom.: 39605 AF XY: 0.769 AC XY: 52804 AN XY: 68658

Gnomad4 AFR exome AF: 0.522

Gnomad4 AMR exome AF: 0.642

Gnomad4 ASJ exome AF: 0.835

Gnomad4 EAS exome AF: 0.373

Gnomad4 SAS exome AF: 0.683

Gnomad4 FIN exome AF: 0.734

Gnomad4 NFE exome AF: 0.822

Gnomad4 OTH exome AF: 0.757

GnomAD4 genome AF: 0.686 AC: 104141 AN: 151826 Hom.: 37526 Cov.: 0 AF XY: 0.680 AC XY: 50433 AN XY: 74202

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.708

Alfa AF: 0.750 Hom.: 5357

Bravo AF: 0.669

Asia WGS AF: 0.481 AC: 1677 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 27, 2018

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Computational scores

Source: dbNSFP v4.3

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: rs147333449; hg19: chr10-28101113;