19-48297081-A-G

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.2019T>C(p.Ser673Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 1,613,386 control chromosomes in the GnomAD database, including 331,731 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27177 hom., cov: 32)

Exomes 𝑓: 0.64 ( 304554 hom. )

Consequence

ODAD1
NM_001364171.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -8.96

Publications

18 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=-1.1).

BP6

Variant 19-48297081-A-G is Benign according to our data. Variant chr19-48297081-A-G is described in ClinVar as Benign. ClinVar VariationId is 262496.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-8.96 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD1	NM_001364171.2 link	c.2019T>C	p.Ser673Ser	synonymous_variant	Exon 16 of 16	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4 link	c.1908T>C	p.Ser636Ser	synonymous_variant	Exon 14 of 14		NP_653178.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD1	ENST00000674294.1 link	c.2019T>C	p.Ser673Ser	synonymous_variant	Exon 16 of 16		NM_001364171.2	ENSP00000501363.1

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89502

AN:

151870

Hom.:

27159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.514

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.653

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.619

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.674

Gnomad OTH

AF:

0.598

GnomAD2 exomes

AF:

0.563

AC:

141230

AN:

250780

AF XY:

0.570

show subpopulations

Gnomad AFR exome

AF:

0.523

Gnomad AMR exome

AF:

0.391

Gnomad ASJ exome

AF:

0.669

Gnomad EAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.617

Gnomad NFE exome

AF:

0.673

Gnomad OTH exome

AF:

0.596

GnomAD4 exome

AF:

0.638

AC:

931918

AN:

1461398

Hom.:

304554

Cov.:

AF XY:

0.633

AC XY:

460424

AN XY:

727046

show subpopulations

African (AFR)

AF:

0.527

AC:

17628

AN:

33476

American (AMR)

AF:

0.403

AC:

18023

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.669

AC:

17480

AN:

26130

East Asian (EAS)

AF:

0.253

AC:

10060

AN:

39698

South Asian (SAS)

AF:

0.467

AC:

40304

AN:

86254

European-Finnish (FIN)

AF:

0.618

AC:

32789

AN:

53060

Middle Eastern (MID)

AF:

0.595

AC:

3422

AN:

5754

European-Non Finnish (NFE)

AF:

0.679

AC:

754947

AN:

1111930

Other (OTH)

AF:

0.617

AC:

37265

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

20506

41013

61519

82026

102532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19136

38272

57408

76544

95680

<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:

0.589

AC:

89566

AN:

151988

Hom.:

27177

Cov.:

AF XY:

0.581

AC XY:

43151

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.529

AC:

21935

AN:

41460

American (AMR)

AF:

0.496

AC:

7579

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.653

AC:

2267

AN:

3472

East Asian (EAS)

AF:

0.268

AC:

1379

AN:

5138

South Asian (SAS)

AF:

0.454

AC:

2188

AN:

4816

European-Finnish (FIN)

AF:

0.619

AC:

6546

AN:

10578

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.674

AC:

45763

AN:

67938

Other (OTH)

AF:

0.595

AC:

1255

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1825

3650

5475

7300

9125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<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:

0.642

Hom.:

45411

Bravo

AF:

0.577

Asia WGS

AF:

0.359

AC:

1253

AN:

3478

EpiCase

AF:

0.667

EpiControl

AF:

0.664

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

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

Dec 09, 2015

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Primary ciliary dyskinesia

Benign:2

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.

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Nov 28, 2018

GeneDx

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

-1.1

CADD

Benign

0.022

(source)

DANN

Benign

0.36

PhyloP100

-9.0

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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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