dbSNP rs2242463: ODAD1:p.Asp306Asp (chr19-48303720-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

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

The NM_001364171.2(ODAD1):c.918C>T(p.Asp306Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,613,800 control chromosomes in the GnomAD database, including 29,201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2525 hom., cov: 32)

Exomes 𝑓: 0.19 ( 26676 hom. )

Consequence

ODAD1
NM_001364171.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.86

Variant links:

Genes affected

ODAD1 (HGNC:26560): (outer dynein arm docking complex subunit 1) This gene encodes a coiled-coil domain-containing protein that is a component of the outer dynein arm docking complex in cilia cells. Mutations in this gene may cause primary ciliary dyskinesia 20. [provided by RefSeq, May 2013]

ODAD1 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=-0.8).

BP6

Variant 19-48303720-G-A is Benign according to our data. Variant chr19-48303720-G-A is described in ClinVar as [Benign]. Clinvar id is 262507.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.86 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD1	NM_001364171.2 link	c.918C>T	p.Asp306Asp	synonymous_variant	Exon 10 of 16	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4 link	c.807C>T	p.Asp269Asp	synonymous_variant	Exon 8 of 14		NP_653178.3	Q96M63-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD1	ENST00000674294.1 link	c.918C>T	p.Asp306Asp	synonymous_variant	Exon 10 of 16		NM_001364171.2	ENSP00000501363.1		A0A6I8PTZ2

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27032

AN:

152040

Hom.:

2523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.170

GnomAD3 exomes

AF:

0.178

AC:

44651

AN:

251178

Hom.:

4340

AF XY:

0.183

AC XY:

24869

AN XY:

135738

show subpopulations

Gnomad AFR exome

AF:

0.155

Gnomad AMR exome

AF:

0.0838

Gnomad ASJ exome

AF:

0.185

Gnomad EAS exome

AF:

0.127

Gnomad SAS exome

AF:

0.183

Gnomad FIN exome

AF:

0.262

Gnomad NFE exome

AF:

0.200

Gnomad OTH exome

AF:

0.171

GnomAD4 exome

AF:

0.187

AC:

273514

AN:

1461642

Hom.:

26676

Cov.:

AF XY:

0.188

AC XY:

136623

AN XY:

727150

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.0870

Gnomad4 ASJ exome

AF:

0.180

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.177

Gnomad4 FIN exome

AF:

0.254

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.178

AC:

27037

AN:

152158

Hom.:

2525

Cov.:

AF XY:

0.180

AC XY:

13387

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.114

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.124

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.260

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.170

Alfa

AF:

0.188

Hom.:

6402

Bravo

AF:

0.167

Asia WGS

AF:

0.150

AC:

523

AN:

3478

EpiCase

AF:

0.189

EpiControl

AF:

0.185

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia

Benign:2

Jul 09, 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. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.97

DANN

Benign

0.88

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