rs60290948
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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.2275-15G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00505 in 1,521,768 control chromosomes in the GnomAD database, including 464 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0065 ( 63 hom., cov: 32)
Exomes 𝑓: 0.0049 ( 401 hom. )
Consequence
DNAH11
NM_001277115.2 splice_polypyrimidine_tract, intron
NM_001277115.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.44
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=-0.85).
BP6
Variant 7-21591170-G-T is Benign according to our data. Variant chr7-21591170-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 226584.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21591170-G-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH11 | NM_001277115.2 | c.2275-15G>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000409508.8 | NP_001264044.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.2275-15G>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001277115.2 | ENSP00000475939 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00653 AC: 994AN: 152116Hom.: 65 Cov.: 32
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GnomAD3 exomes AF: 0.0144 AC: 2675AN: 186316Hom.: 185 AF XY: 0.0131 AC XY: 1323AN XY: 100658
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GnomAD4 exome AF: 0.00489 AC: 6695AN: 1369534Hom.: 401 Cov.: 30 AF XY: 0.00481 AC XY: 3245AN XY: 673986
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GnomAD4 genome AF: 0.00653 AC: 994AN: 152234Hom.: 63 Cov.: 32 AF XY: 0.00755 AC XY: 562AN XY: 74438
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | 2275-15G>T in intron 13 of DNAH11: This variant is not expected to have clinical significance because it has been identified in 21.5% (43/200) of Han Chinese ch romosomes from a broad population by the 1000 Genomes Project (http://www.ncbi.n lm.nih.gov/projects/SNP; dbSNP rs60290948). - |
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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