Genetic Variant ODAD1:c.1404+20C>A (chr19-48298157-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001364171.2(ODAD1):c.1404+20C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,611,326 control chromosomes in the GnomAD database, including 29,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2514 hom., cov: 31)

Exomes 𝑓: 0.19 ( 26599 hom. )

Consequence

ODAD1
NM_001364171.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.72

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: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 19-48298157-G-T is Benign according to our data. Variant chr19-48298157-G-T is described in ClinVar as Benign. ClinVar VariationId is 262485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364171.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD1	NM_001364171.2	MANE Select	c.1404+20C>A		intron	N/A	NP_001351100.1	A0A6I8PTZ2
	ODAD1	NM_144577.4		c.1293+20C>A		intron	N/A	NP_653178.3	Q96M63-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ODAD1	ENST00000674294.1	MANE Select	c.1404+20C>A	intron	N/A	ENSP00000501363.1	A0A6I8PTZ2
ODAD1	ENST00000315396.7	TSL:1	c.1293+20C>A	intron	N/A	ENSP00000318429.7	Q96M63-1
ODAD1	ENST00000859784.1		c.1464+20C>A	intron	N/A	ENSP00000529843.1

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

26945

AN:

151666

Hom.:

2512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.169

GnomAD2 exomes

AF:

0.177

AC:

44188

AN:

249520

AF XY:

0.183

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.0837

Gnomad ASJ exome

AF:

0.185

Gnomad EAS exome

AF:

0.126

Gnomad FIN exome

AF:

0.261

Gnomad NFE exome

AF:

0.200

Gnomad OTH exome

AF:

0.171

GnomAD4 exome

AF:

0.187

AC:

272823

AN:

1459542

Hom.:

26599

Cov.:

AF XY:

0.188

AC XY:

136307

AN XY:

726144

show subpopulations

African (AFR)

AF:

0.153

AC:

5108

AN:

33466

American (AMR)

AF:

0.0869

AC:

3886

AN:

44706

Ashkenazi Jewish (ASJ)

AF:

0.180

AC:

4711

AN:

26116

East Asian (EAS)

AF:

0.115

AC:

4564

AN:

39694

South Asian (SAS)

AF:

0.177

AC:

15273

AN:

86238

European-Finnish (FIN)

AF:

0.252

AC:

13042

AN:

51662

Middle Eastern (MID)

AF:

0.183

AC:

1056

AN:

5768

European-Non Finnish (NFE)

AF:

0.193

AC:

214588

AN:

1111534

Other (OTH)

AF:

0.176

AC:

10595

AN:

60358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

11050

22099

33149

44198

55248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7346

14692

22038

29384

36730

<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:

0.178

AC:

26947

AN:

151784

Hom.:

2514

Cov.:

AF XY:

0.180

AC XY:

13329

AN XY:

74148

show subpopulations

African (AFR)

AF:

0.156

AC:

6447

AN:

41384

American (AMR)

AF:

0.114

AC:

1740

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

614

AN:

3470

East Asian (EAS)

AF:

0.124

AC:

636

AN:

5116

South Asian (SAS)

AF:

0.176

AC:

844

AN:

4800

European-Finnish (FIN)

AF:

0.260

AC:

2746

AN:

10556

Middle Eastern (MID)

AF:

0.233

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.197

AC:

13382

AN:

67888

Other (OTH)

AF:

0.170

AC:

358

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1105

2211

3316

4422

5527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.136

Hom.:

337

Bravo

AF:

0.167

Asia WGS

AF:

0.149

AC:

521

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

not specified (1)

Primary ciliary dyskinesia (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.040

(source)

DANN

Benign

0.44

PhyloP100

-2.7

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over