chr19-11426557-G-A
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_145045.5(ODAD3):c.729C>T(p.Asn243=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,614,060 control chromosomes in the GnomAD database, including 177 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.011 ( 17 hom., cov: 31)
Exomes 𝑓: 0.014 ( 160 hom. )
Consequence
ODAD3
NM_145045.5 synonymous
NM_145045.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.162
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 19-11426557-G-A is Benign according to our data. Variant chr19-11426557-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 241946.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.162 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0115 (1747/152218) while in subpopulation NFE AF= 0.0163 (1107/67996). AF 95% confidence interval is 0.0155. There are 17 homozygotes in gnomad4. There are 824 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODAD3 | NM_145045.5 | c.729C>T | p.Asn243= | synonymous_variant | 6/13 | ENST00000356392.9 | |
ODAD3 | NM_001302453.1 | c.567C>T | p.Asn189= | synonymous_variant | 6/13 | ||
ODAD3 | NM_001302454.2 | c.549C>T | p.Asn183= | synonymous_variant | 4/11 | ||
ODAD3 | XM_017026241.2 | c.729C>T | p.Asn243= | synonymous_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAD3 | ENST00000356392.9 | c.729C>T | p.Asn243= | synonymous_variant | 6/13 | 1 | NM_145045.5 | P2 | |
ODAD3 | ENST00000591179.5 | c.549C>T | p.Asn183= | synonymous_variant | 4/11 | 1 | A2 | ||
ODAD3 | ENST00000586836.5 | c.156C>T | p.Asn52= | synonymous_variant | 6/13 | 2 | A2 | ||
ODAD3 | ENST00000591345.5 | c.*648C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0115 AC: 1743AN: 152100Hom.: 17 Cov.: 31
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GnomAD3 exomes AF: 0.0123 AC: 3061AN: 249360Hom.: 20 AF XY: 0.0128 AC XY: 1732AN XY: 135300
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GnomAD4 exome AF: 0.0140 AC: 20503AN: 1461842Hom.: 160 Cov.: 33 AF XY: 0.0141 AC XY: 10268AN XY: 727224
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GnomAD4 genome AF: 0.0115 AC: 1747AN: 152218Hom.: 17 Cov.: 31 AF XY: 0.0111 AC XY: 824AN XY: 74420
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 30 Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 13, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2020 | - - |
Computational scores
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BayesDel_noAF
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CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at