rs34540645

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001364171.2(ODAD1):c.1176G>A(p.Ser392Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 1,613,612 control chromosomes in the GnomAD database, including 6,019 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 386 hom., cov: 32)

Exomes 𝑓: 0.082 ( 5633 hom. )

Consequence

ODAD1
NM_001364171.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.35

Publications

6 publications found

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 Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 20
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ODAD1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 19-48302758-C-T is Benign according to our data. Variant chr19-48302758-C-T is described in ClinVar as Benign. ClinVar VariationId is 262483.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD1	NM_001364171.2 link	c.1176G>A	p.Ser392Ser	synonymous_variant	Exon 12 of 16	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4 link	c.1065G>A	p.Ser355Ser	synonymous_variant	Exon 10 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.1176G>A	p.Ser392Ser	synonymous_variant	Exon 12 of 16		NM_001364171.2	ENSP00000501363.1		A0A6I8PTZ2

Frequencies

GnomAD3 genomes

AF:

0.0601

AC:

9146

AN:

152202

Hom.:

386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0169

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.0669

Gnomad ASJ

AF:

0.0905

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0221

Gnomad FIN

AF:

0.0392

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0929

Gnomad OTH

AF:

0.0765

GnomAD2 exomes

AF:

0.0604

AC:

15094

AN:

249964

AF XY:

0.0609

show subpopulations

Gnomad AFR exome

AF:

0.0144

Gnomad AMR exome

AF:

0.0472

Gnomad ASJ exome

AF:

0.0940

Gnomad EAS exome

AF:

0.000327

Gnomad FIN exome

AF:

0.0399

Gnomad NFE exome

AF:

0.0909

Gnomad OTH exome

AF:

0.0734

GnomAD4 exome

AF:

0.0823

AC:

120296

AN:

1461292

Hom.:

5633

Cov.:

AF XY:

0.0805

AC XY:

58551

AN XY:

726974

show subpopulations

African (AFR)

AF:

0.0122

AC:

410

AN:

33480

American (AMR)

AF:

0.0502

AC:

2245

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0946

AC:

2472

AN:

26132

East Asian (EAS)

AF:

0.000176

AC:

AN:

39700

South Asian (SAS)

AF:

0.0242

AC:

2091

AN:

86256

European-Finnish (FIN)

AF:

0.0412

AC:

2179

AN:

52906

Middle Eastern (MID)

AF:

0.0501

AC:

289

AN:

5768

European-Non Finnish (NFE)

AF:

0.0950

AC:

105607

AN:

1111948

Other (OTH)

AF:

0.0827

AC:

4996

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

6113

12226

18338

24451

30564

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3748

7496

11244

14992

18740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0600

AC:

9143

AN:

152320

Hom.:

386

Cov.:

AF XY:

0.0573

AC XY:

4269

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.0168

AC:

699

AN:

41578

American (AMR)

AF:

0.0668

AC:

1021

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0905

AC:

314

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5186

South Asian (SAS)

AF:

0.0223

AC:

108

AN:

4834

European-Finnish (FIN)

AF:

0.0392

AC:

416

AN:

10622

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0929

AC:

6316

AN:

68022

Other (OTH)

AF:

0.0757

AC:

160

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

447

895

1342

1790

2237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0791

Hom.:

397

Bravo

AF:

0.0603

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0966

EpiControl

AF:

0.0963

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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. -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Nov 27, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

-0.78

CADD

Benign

0.12

(source)

DANN

Benign

0.57

PhyloP100

-3.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over