rs183031009
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001277115.2(DNAH11):c.13406G>A(p.Arg4469Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000221 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001277115.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH11 | NM_001277115.2 | c.13406G>A | p.Arg4469Lys | missense_variant | 82/82 | ENST00000409508.8 | |
CDCA7L | NM_018719.5 | c.*1213C>T | 3_prime_UTR_variant | 10/10 | ENST00000406877.8 | ||
CDCA7L | NM_001127370.3 | c.*1213C>T | 3_prime_UTR_variant | 11/11 | |||
CDCA7L | NM_001127371.3 | c.*1213C>T | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.13406G>A | p.Arg4469Lys | missense_variant | 82/82 | 5 | NM_001277115.2 | P1 | |
CDCA7L | ENST00000406877.8 | c.*1213C>T | 3_prime_UTR_variant | 10/10 | 1 | NM_018719.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00109 AC: 166AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000229 AC: 57AN: 248996Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135150
GnomAD4 exome AF: 0.000131 AC: 191AN: 1461680Hom.: 0 Cov.: 33 AF XY: 0.000106 AC XY: 77AN XY: 727114
GnomAD4 genome ? AF: 0.00109 AC: 166AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.00110 AC XY: 82AN XY: 74480
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
DNAH11-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at