rs370978492
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_145045.5(ODAD3):c.366+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000418 in 1,613,840 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00032 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00043 ( 2 hom. )
Consequence
ODAD3
NM_145045.5 intron
NM_145045.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.505
Publications
1 publications found
Genes affected
ODAD3 (HGNC:28303): (outer dynein arm docking complex subunit 3) This gene encodes a protein containing coiled-coil domains. The encoded protein functions in outer dynein arm assembly and is required for motile cilia function. Mutations in this gene result in primary ciliary dyskinesia. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]
ODAD3 Gene-Disease associations (from GenCC):
- primary ciliary dyskinesia 30Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, G2P
- primary ciliary dyskinesiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 19-11430890-G-A is Benign according to our data. Variant chr19-11430890-G-A is described in CliVar as Likely_benign. Clinvar id is 477981.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11430890-G-A is described in CliVar as Likely_benign. Clinvar id is 477981.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11430890-G-A is described in CliVar as Likely_benign. Clinvar id is 477981.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11430890-G-A is described in CliVar as Likely_benign. Clinvar id is 477981.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11430890-G-A is described in CliVar as Likely_benign. Clinvar id is 477981.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11430890-G-A is described in CliVar as Likely_benign. Clinvar id is 477981.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11430890-G-A is described in CliVar as Likely_benign. Clinvar id is 477981.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.000316 (48/152034) while in subpopulation NFE AF = 0.000632 (43/68018). AF 95% confidence interval is 0.000482. There are 0 homozygotes in GnomAd4. There are 17 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
BS2
High Homozygotes in GnomAdExome4 at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ODAD3 | NM_145045.5 | c.366+9C>T | intron_variant | Intron 2 of 12 | ENST00000356392.9 | NP_659482.3 | ||
ODAD3 | NM_001302453.1 | c.204+9C>T | intron_variant | Intron 2 of 12 | NP_001289382.1 | |||
ODAD3 | NM_001302454.2 | c.366+9C>T | intron_variant | Intron 2 of 10 | NP_001289383.1 | |||
ODAD3 | XM_017026241.2 | c.366+9C>T | intron_variant | Intron 2 of 8 | XP_016881730.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000316 AC: 48AN: 152034Hom.: 0 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
48
AN:
152034
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000160 AC: 40AN: 249436 AF XY: 0.000177 show subpopulations
GnomAD2 exomes
AF:
AC:
40
AN:
249436
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000429 AC: 627AN: 1461806Hom.: 2 Cov.: 35 AF XY: 0.000422 AC XY: 307AN XY: 727188 show subpopulations
GnomAD4 exome
AF:
AC:
627
AN:
1461806
Hom.:
Cov.:
35
AF XY:
AC XY:
307
AN XY:
727188
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33480
American (AMR)
AF:
AC:
2
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39696
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53406
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
610
AN:
1111950
Other (OTH)
AF:
AC:
14
AN:
60394
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
34
69
103
138
172
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
28
56
84
112
140
<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: 0.000316 AC: 48AN: 152034Hom.: 0 Cov.: 30 AF XY: 0.000229 AC XY: 17AN XY: 74264 show subpopulations
GnomAD4 genome
AF:
AC:
48
AN:
152034
Hom.:
Cov.:
30
AF XY:
AC XY:
17
AN XY:
74264
show subpopulations
African (AFR)
AF:
AC:
4
AN:
41378
American (AMR)
AF:
AC:
1
AN:
15244
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5184
South Asian (SAS)
AF:
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10594
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
43
AN:
68018
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.481
Heterozygous variant carriers
0
3
6
10
13
16
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 30 Benign:1
Aug 28, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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