rs886038464
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001277115.2(DNAH11):c.3766-10C>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000015 ( 0 hom., cov: 16)
Exomes 𝑓: 0.000027 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DNAH11
NM_001277115.2 splice_polypyrimidine_tract, intron
NM_001277115.2 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0003318
2
Clinical Significance
Conservation
PhyloP100: -0.752
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 7-21606637-C-A is Benign according to our data. Variant chr7-21606637-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 257886.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-21606637-C-A is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH11 | NM_001277115.2 | c.3766-10C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000409508.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.3766-10C>A | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001277115.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 68036Hom.: 0 Cov.: 16 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000267 AC: 20AN: 749464Hom.: 0 Cov.: 24 AF XY: 0.0000291 AC XY: 11AN XY: 377554
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000147 AC: 1AN: 68078Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0AN XY: 31810
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at