chr19-48304110-C-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001364171.2(ODAD1):c.696G>T(p.Leu232Leu) 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 1,611,918 control chromosomes in the GnomAD database, including 29,165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2536 hom., cov: 33)

Exomes 𝑓: 0.19 ( 26629 hom. )

Consequence

ODAD1
NM_001364171.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.206

Publications

12 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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 19-48304110-C-A is Benign according to our data. Variant chr19-48304110-C-A is described in ClinVar as [Benign]. Clinvar id is 262504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.206 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.696G>T	p.Leu232Leu	synonymous_variant	Exon 9 of 16	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4 link	c.585G>T	p.Leu195Leu	synonymous_variant	Exon 7 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.696G>T	p.Leu232Leu	synonymous_variant	Exon 9 of 16		NM_001364171.2	ENSP00000501363.1		A0A6I8PTZ2

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27146

AN:

152066

Hom.:

2534

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.168

GnomAD2 exomes

AF:

0.178

AC:

44368

AN:

249752

AF XY:

0.183

show subpopulations

Gnomad AFR exome

AF:

0.158

Gnomad AMR exome

AF:

0.0839

Gnomad ASJ exome

AF:

0.185

Gnomad EAS exome

AF:

0.127

Gnomad FIN exome

AF:

0.262

Gnomad NFE exome

AF:

0.200

Gnomad OTH exome

AF:

0.172

GnomAD4 exome

AF:

0.187

AC:

273169

AN:

1459734

Hom.:

26629

Cov.:

AF XY:

0.188

AC XY:

136349

AN XY:

725938

show subpopulations

African (AFR)

AF:

0.157

AC:

5251

AN:

33456

American (AMR)

AF:

0.0873

AC:

3898

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.180

AC:

4711

AN:

26108

East Asian (EAS)

AF:

0.115

AC:

4559

AN:

39654

South Asian (SAS)

AF:

0.175

AC:

15098

AN:

86236

European-Finnish (FIN)

AF:

0.254

AC:

13346

AN:

52586

Middle Eastern (MID)

AF:

0.183

AC:

1054

AN:

5760

European-Non Finnish (NFE)

AF:

0.193

AC:

214623

AN:

1110940

Other (OTH)

AF:

0.176

AC:

10629

AN:

60324

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

13427

26854

40282

53709

67136

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.178

AC:

27152

AN:

152184

Hom.:

2536

Cov.:

AF XY:

0.181

AC XY:

13439

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.160

AC:

6627

AN:

41530

American (AMR)

AF:

0.114

AC:

1745

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

614

AN:

3466

East Asian (EAS)

AF:

0.123

AC:

638

AN:

5166

South Asian (SAS)

AF:

0.174

AC:

842

AN:

4830

European-Finnish (FIN)

AF:

0.260

AC:

2752

AN:

10598

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.197

AC:

13396

AN:

67988

Other (OTH)

AF:

0.169

AC:

356

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1169

2337

3506

4674

5843

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.186

Hom.:

1159

Bravo

AF:

0.168

Asia WGS

AF:

0.151

AC:

527

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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. -

not provided

Benign:2

Feb 22, 2019

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

-0.40

CADD

Benign

4.6

(source)

DANN

Benign

0.81

PhyloP100

0.21

Mutation Taster

=100/0

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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chr19-48304110-C-A

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