Variant chr10-27812382-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018076.5(ODAD2):c.*130A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 765,212 control chromosomes in the GnomAD database, including 6,600 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.098 ( 978 hom., cov: 33)

Exomes 𝑓: 0.13 ( 5622 hom. )

Consequence

ODAD2
NM_018076.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.509

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 10-27812382-T-C is Benign according to our data. Variant chr10-27812382-T-C is described in ClinVar as [Benign]. Clinvar id is 1222323.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODAD2	NM_018076.5 linkuse as main transcript	c.*130A>G		3_prime_UTR_variant	20/20	ENST00000305242.10	NP_060546.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODAD2	ENST00000305242.10 linkuse as main transcript	c.*130A>G		3_prime_UTR_variant	20/20	1	NM_018076.5	ENSP00000306410	P1	Q5T2S8-1

Frequencies

GnomAD3 genomes

AF:

0.0981

AC:

14923

AN:

152190

Hom.:

978

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0258

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.0799

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.00211

Gnomad SAS

AF:

0.0770

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.0913

GnomAD4 exome

AF:

0.130

AC:

79807

AN:

612904

Hom.:

5622

Cov.:

AF XY:

0.128

AC XY:

41201

AN XY:

321164

show subpopulations

Gnomad4 AFR exome

AF:

0.0223

Gnomad4 AMR exome

AF:

0.0776

Gnomad4 ASJ exome

AF:

0.120

Gnomad4 EAS exome

AF:

0.000722

Gnomad4 SAS exome

AF:

0.0872

Gnomad4 FIN exome

AF:

0.145

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.0980

AC:

14926

AN:

152308

Hom.:

978

Cov.:

AF XY:

0.0967

AC XY:

7203

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0257

Gnomad4 AMR

AF:

0.0801

Gnomad4 ASJ

AF:

0.128

Gnomad4 EAS

AF:

0.00212

Gnomad4 SAS

AF:

0.0771

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.144

Gnomad4 OTH

AF:

0.0908

Alfa

AF:

0.133

Hom.:

1535

Bravo

AF:

0.0905

Asia WGS

AF:

0.0390

AC:

134

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 16, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.0

DANN

Benign

0.51

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

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