rs729657
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001277115.2(DNAH11):c.8155-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 1,609,344 control chromosomes in the GnomAD database, including 6,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.056 ( 338 hom., cov: 33)
Exomes 𝑓: 0.084 ( 5674 hom. )
Consequence
DNAH11
NM_001277115.2 intron
NM_001277115.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.211
Genes affected
DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]
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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 (BayesDel_noAF=-0.75).
BP6
?
Variant 7-21744419-C-T is Benign according to our data. Variant chr7-21744419-C-T is described in ClinVar as [Benign]. Clinvar id is 257934.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21744419-C-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0852 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH11 | NM_001277115.2 | c.8155-19C>T | intron_variant | ENST00000409508.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.8155-19C>T | intron_variant | 5 | NM_001277115.2 | P1 | |||
DNAH11 | ENST00000605912.1 | c.475-451C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0563 AC: 8567AN: 152068Hom.: 336 Cov.: 33
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GnomAD3 exomes AF: 0.0652 AC: 16015AN: 245636Hom.: 673 AF XY: 0.0675 AC XY: 8988AN XY: 133104
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GnomAD4 exome AF: 0.0841 AC: 122612AN: 1457156Hom.: 5674 Cov.: 31 AF XY: 0.0838 AC XY: 60693AN XY: 724598
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GnomAD4 genome ? AF: 0.0563 AC: 8569AN: 152188Hom.: 338 Cov.: 33 AF XY: 0.0550 AC XY: 4093AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 05, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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