10-27812184-CTTT-C

Variant names:

• chr10-27812184-CTTT-C
• rs147333449
• NM_018076.5:c.*325_*327delAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018076.5(ODAD2):​c.*325_*327delAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ODAD2 NM_018076.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.55
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 23

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, G2P
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018076.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2	NM_018076.5	MANE Select	c.*325_*327delAAA		3_prime_UTR	Exon 20 of 20	NP_060546.2
	ODAD2	NM_001290020.2		c.*325_*327delAAA		3_prime_UTR	Exon 20 of 20	NP_001276949.1	A0A140VKF7
	ODAD2	NM_001312689.2		c.*325_*327delAAA		3_prime_UTR	Exon 15 of 15	NP_001299618.1	A0A5F9ZH22

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2	ENST00000305242.10	TSL:1 MANE Select	c.*325_*327delAAA		3_prime_UTR	Exon 20 of 20	ENSP00000306410.5	Q5T2S8-1
	ODAD2	ENST00000852623.1		c.*325_*327delAAA		3_prime_UTR	Exon 20 of 20	ENSP00000522682.1
	ODAD2	ENST00000923084.1		c.*325_*327delAAA		3_prime_UTR	Exon 20 of 20	ENSP00000593143.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 129082 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 68810

African (AFR) AF: 0.00 AC: 0 AN: 1766

American (AMR) AF: 0.00 AC: 0 AN: 1982

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3590

East Asian (EAS) AF: 0.00 AC: 0 AN: 2306

South Asian (SAS) AF: 0.00 AC: 0 AN: 19376

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7686

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 590

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 84328

Other (OTH) AF: 0.00 AC: 0 AN: 7458

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.5

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

Other links and lift over

dbSNP: rs147333449; hg19: chr10-28101113;