chr10-27939936-A-G

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_018076.5(ODAD2):c.2058T>C(p.Asn686Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 1,608,196 control chromosomes in the GnomAD database, including 227,820 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 20574 hom., cov: 31)

Exomes 𝑓: 0.53 ( 207246 hom. )

Consequence

ODAD2
NM_018076.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.620

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 10-27939936-A-G is Benign according to our data. Variant chr10-27939936-A-G is described in ClinVar as [Benign]. Clinvar id is 260994.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.62 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD2	NM_018076.5 link	c.2058T>C	p.Asn686Asn	synonymous_variant	Exon 14 of 20	ENST00000305242.10	NP_060546.2	Q5T2S8-1A0A140VKF7B7Z7Y0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD2	ENST00000305242.10 link	c.2058T>C	p.Asn686Asn	synonymous_variant	Exon 14 of 20	1	NM_018076.5	ENSP00000306410.5		Q5T2S8-1

Frequencies

GnomAD3 genomes

AF:

0.517

AC:

78457

AN:

151680

Hom.:

20557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.456

Gnomad AMI

AF:

0.605

Gnomad AMR

AF:

0.564

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.529

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.521

Gnomad MID

AF:

0.640

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.555

GnomAD3 exomes

AF:

0.535

AC:

132042

AN:

246658

Hom.:

35805

AF XY:

0.542

AC XY:

72374

AN XY:

133532

show subpopulations

Gnomad AFR exome

AF:

0.450

Gnomad AMR exome

AF:

0.515

Gnomad ASJ exome

AF:

0.536

Gnomad EAS exome

AF:

0.540

Gnomad SAS exome

AF:

0.601

Gnomad FIN exome

AF:

0.535

Gnomad NFE exome

AF:

0.534

Gnomad OTH exome

AF:

0.555

GnomAD4 exome

AF:

0.532

AC:

774801

AN:

1456396

Hom.:

207246

Cov.:

AF XY:

0.535

AC XY:

387671

AN XY:

724654

show subpopulations

Gnomad4 AFR exome

AF:

0.453

Gnomad4 AMR exome

AF:

0.522

Gnomad4 ASJ exome

AF:

0.533

Gnomad4 EAS exome

AF:

0.542

Gnomad4 SAS exome

AF:

0.602

Gnomad4 FIN exome

AF:

0.530

Gnomad4 NFE exome

AF:

0.528

Gnomad4 OTH exome

AF:

0.539

GnomAD4 genome

AF:

0.517

AC:

78513

AN:

151800

Hom.:

20574

Cov.:

AF XY:

0.520

AC XY:

38595

AN XY:

74164

show subpopulations

Gnomad4 AFR

AF:

0.457

Gnomad4 AMR

AF:

0.563

Gnomad4 ASJ

AF:

0.531

Gnomad4 EAS

AF:

0.529

Gnomad4 SAS

AF:

0.589

Gnomad4 FIN

AF:

0.521

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.552

Alfa

AF:

0.537

Hom.:

45122

Bravo

AF:

0.515

Asia WGS

AF:

0.510

AC:

1779

AN:

3478

EpiCase

AF:

0.540

EpiControl

AF:

0.547

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Primary ciliary dyskinesia 23

Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia

Benign:1

Jul 07, 2016

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.15

DANN

Benign

0.27

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