rs61739927
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_145045.5(ODAD3):c.424C>G(p.Leu142Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0085 in 1,614,046 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.012 ( 26 hom., cov: 32)
Exomes 𝑓: 0.0081 ( 64 hom. )
Consequence
ODAD3
NM_145045.5 missense
NM_145045.5 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 1.07
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.010106593).
BP6
Variant 19-11430719-G-C is Benign according to our data. Variant chr19-11430719-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 414138.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11430719-G-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0119 (1816/152174) while in subpopulation AFR AF = 0.0233 (966/41522). AF 95% confidence interval is 0.022. There are 26 homozygotes in GnomAd4. There are 921 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
BS2
High Homozygotes in GnomAd4 at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ODAD3 | NM_145045.5 | c.424C>G | p.Leu142Val | missense_variant | Exon 3 of 13 | ENST00000356392.9 | NP_659482.3 | |
ODAD3 | NM_001302453.1 | c.262C>G | p.Leu88Val | missense_variant | Exon 3 of 13 | NP_001289382.1 | ||
ODAD3 | XM_017026241.2 | c.424C>G | p.Leu142Val | missense_variant | Exon 3 of 9 | XP_016881730.1 | ||
ODAD3 | NM_001302454.2 | c.366+180C>G | intron_variant | Intron 2 of 10 | NP_001289383.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0118 AC: 1787AN: 152056Hom.: 23 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1787
AN:
152056
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.00794 AC: 1981AN: 249508 AF XY: 0.00825 show subpopulations
GnomAD2 exomes
AF:
AC:
1981
AN:
249508
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.00814 AC: 11900AN: 1461872Hom.: 64 Cov.: 31 AF XY: 0.00830 AC XY: 6038AN XY: 727234 show subpopulations
GnomAD4 exome
AF:
AC:
11900
AN:
1461872
Hom.:
Cov.:
31
AF XY:
AC XY:
6038
AN XY:
727234
Gnomad4 AFR exome
AF:
AC:
844
AN:
33480
Gnomad4 AMR exome
AF:
AC:
127
AN:
44724
Gnomad4 ASJ exome
AF:
AC:
1
AN:
26136
Gnomad4 EAS exome
AF:
AC:
163
AN:
39700
Gnomad4 SAS exome
AF:
AC:
1117
AN:
86258
Gnomad4 FIN exome
AF:
AC:
291
AN:
53420
Gnomad4 NFE exome
AF:
AC:
8844
AN:
1111994
Gnomad4 Remaining exome
AF:
AC:
470
AN:
60392
Heterozygous variant carriers
0
650
1301
1951
2602
3252
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
372
744
1116
1488
1860
<30
30-35
35-40
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55-60
60-65
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>80
Age
GnomAD4 genome AF: 0.0119 AC: 1816AN: 152174Hom.: 26 Cov.: 32 AF XY: 0.0124 AC XY: 921AN XY: 74386 show subpopulations
GnomAD4 genome
AF:
AC:
1816
AN:
152174
Hom.:
Cov.:
32
AF XY:
AC XY:
921
AN XY:
74386
Gnomad4 AFR
AF:
AC:
0.0232648
AN:
0.0232648
Gnomad4 AMR
AF:
AC:
0.00524315
AN:
0.00524315
Gnomad4 ASJ
AF:
AC:
0.000288184
AN:
0.000288184
Gnomad4 EAS
AF:
AC:
0.00793651
AN:
0.00793651
Gnomad4 SAS
AF:
AC:
0.013076
AN:
0.013076
Gnomad4 FIN
AF:
AC:
0.00735294
AN:
0.00735294
Gnomad4 NFE
AF:
AC:
0.00771855
AN:
0.00771855
Gnomad4 OTH
AF:
AC:
0.00947867
AN:
0.00947867
Heterozygous variant carriers
0
91
182
272
363
454
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
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26
52
78
104
130
<30
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Age
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
43
ALSPAC
AF:
AC:
21
ESP6500AA
AF:
AC:
91
ESP6500EA
AF:
AC:
59
ExAC
AF:
AC:
1015
Asia WGS
AF:
AC:
53
AN:
3478
EpiCase
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EpiControl
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 30 Benign:2
Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Nov 09, 2023
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
not provided Benign:2
Apr 21, 2020
GeneDx
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Mutation Taster
=298/2
polymorphism
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