rs189569144
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001277115.2(DNAH11):c.2824C>A(p.Pro942Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000248 in 1,613,464 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00025 ( 3 hom. )
Consequence
DNAH11
NM_001277115.2 missense
NM_001277115.2 missense
Scores
3
5
10
Clinical Significance
Conservation
PhyloP100: 5.71
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.05141291).
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.2824C>A | p.Pro942Thr | missense_variant | 15/82 | 5 | NM_001277115.2 | ENSP00000475939.1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 151934Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000503 AC: 125AN: 248476Hom.: 0 AF XY: 0.000542 AC XY: 73AN XY: 134800
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GnomAD4 exome AF: 0.000249 AC: 364AN: 1461408Hom.: 3 Cov.: 32 AF XY: 0.000307 AC XY: 223AN XY: 726960
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GnomAD4 genome AF: 0.000237 AC: 36AN: 152056Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74346
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:5Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:3Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Institute Of Molecular Biology And Genetics, Federal Almazov National Medical Research Centre | Dec 11, 2023 | This sequence change replaces proline with threonine at evolutionary conserved position 942 of the DNAH11 protein (p.Pro942Thr). The c.2824C>A has a low allele frequency in gnomAD Genomes (Version 3.1.2: ƒ = 0.000237) and several ClinVar submissions with conflicting interpretations of pathogenicity (variation ID 359618). The patient possessed the c.2824C>A variant in trans with another rare missense variant in DNAH11 (c.2966G>A, p.Arg989Gln). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 16, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2017 | The p.P942T variant (also known as c.2824C>A), located in coding exon 15 of the DNAH11 gene, results from a C to A substitution at nucleotide position 2824. The proline at codon 942 is replaced by threonine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | DNAH11: PM2, BP4 - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 24, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
.;.;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
.;.;M
PrimateAI
Benign
T
PROVEAN
Pathogenic
.;D;.
REVEL
Uncertain
Sift
Benign
.;D;.
Polyphen
1.0
.;.;D
Vest4
MVP
ClinPred
T
GERP RS
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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