19-11434872-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145045.5(ODAD3):c.145A>C(p.Thr49Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0049 in 1,614,098 control chromosomes in the GnomAD database, including 338 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.025 ( 150 hom., cov: 33)
Exomes 𝑓: 0.0028 ( 188 hom. )
Consequence
ODAD3
NM_145045.5 missense
NM_145045.5 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.131
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 made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.00212273).
BP6
?
Variant 19-11434872-T-G is Benign according to our data. Variant chr19-11434872-T-G is described in ClinVar as [Benign]. Clinvar id is 414144.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0847 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODAD3 | NM_145045.5 | c.145A>C | p.Thr49Pro | missense_variant | 1/13 | ENST00000356392.9 | |
ODAD3 | NM_001302454.2 | c.145A>C | p.Thr49Pro | missense_variant | 1/11 | ||
ODAD3 | XM_017026241.2 | c.145A>C | p.Thr49Pro | missense_variant | 1/9 | ||
ODAD3 | NM_001302453.1 | c.82+818A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAD3 | ENST00000356392.9 | c.145A>C | p.Thr49Pro | missense_variant | 1/13 | 1 | NM_145045.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0251 AC: 3824AN: 152122Hom.: 148 Cov.: 33
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GnomAD3 exomes AF: 0.00646 AC: 1611AN: 249490Hom.: 72 AF XY: 0.00493 AC XY: 668AN XY: 135372
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GnomAD4 exome AF: 0.00278 AC: 4070AN: 1461856Hom.: 188 Cov.: 31 AF XY: 0.00243 AC XY: 1770AN XY: 727224
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GnomAD4 genome ? AF: 0.0252 AC: 3844AN: 152242Hom.: 150 Cov.: 33 AF XY: 0.0240 AC XY: 1789AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 30 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at