rs372647560

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_018076.5(ODAD2):c.2610+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000938 in 1,599,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000097 ( 0 hom. )

Consequence

ODAD2
NM_018076.5 splice_region, intron

Scores

Splicing: ADA: 0.00001270

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.05

Publications

0 publications found

Variant links:

Genes affected

ODAD2 (HGNC:25583): (outer dynein arm docking complex subunit 2) The protein encoded by this gene contains ten Armadillo repeat motifs (ARMs) and one HEAT repeat, and is thought to be involved in ciliary and flagellar movement. This protein has been shown to localize to the ciliary axonemes and at the ciliary base of respiratory cells. Studies indicate that mutations in this gene cause partial outer dynein arm (ODA) defects in respiratory cilia. The cilia of cells with mutations in this gene displayed either reduced ciliary beat frequency and amplitude, or, complete immotility. Some individuals with primary ciliary dyskensia (PCD) have been shown to have mutations in this gene. PCD is characterized by chronic airway disease and left/right body asymmetry defects. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

ODAD2 Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 23
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ODAD2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 10-27907655-G-A is Benign according to our data. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27907655-G-A is described in CliVar as Likely_benign. Clinvar id is 2906820.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD2	NM_018076.5 link	c.2610+8C>T		splice_region_variant, intron_variant	Intron 17 of 19	ENST00000305242.10	NP_060546.2	Q5T2S8-1A0A140VKF7B7Z7Y0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD2	ENST00000305242.10 link	c.2610+8C>T		splice_region_variant, intron_variant	Intron 17 of 19	1	NM_018076.5	ENSP00000306410.5		Q5T2S8-1

Frequencies

GnomAD3 genomes

AF:

0.0000131

AC:

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000319

AC:

AN:

250392

AF XY:

0.0000370

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000219

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000177

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000967

AC:

AN:

1447140

Hom.:

Cov.:

AF XY:

0.00000694

AC XY:

AN XY:

720888

show subpopulations

African (AFR)

AF:

0.0000904

AC:

AN:

33182

American (AMR)

AF:

0.00

AC:

AN:

44668

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26030

East Asian (EAS)

AF:

0.0000506

AC:

AN:

39522

South Asian (SAS)

AF:

0.0000349

AC:

AN:

85922

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53348

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5726

European-Non Finnish (NFE)

AF:

0.00000546

AC:

AN:

1098866

Other (OTH)

AF:

0.00

AC:

AN:

59876

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.00000657

AC:

AN:

152292

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.0000241

AC:

AN:

41572

American (AMR)

AF:

0.00

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5176

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68028

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000264

EpiCase

AF:

0.00

EpiControl

AF:

0.0000594

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia 23

Benign:1

Mar 17, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.92

CADD

Benign

0.10

(source)

DANN

Benign

0.78

PhyloP100

-3.0

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000013

dbscSNV1_RF

Benign

0.0

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

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over