rs113653972
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001277115.2(DNAH11):c.13076G>A(p.Arg4359Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000387 in 1,613,944 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R4359G) has been classified as Benign.
Frequency
Consequence
NM_001277115.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH11 | NM_001277115.2 | c.13076G>A | p.Arg4359Gln | missense_variant | 80/82 | ENST00000409508.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.13076G>A | p.Arg4359Gln | missense_variant | 80/82 | 5 | NM_001277115.2 | P1 | |
DNAH11 | ENST00000479878.1 | n.447G>A | non_coding_transcript_exon_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00191 AC: 291AN: 152144Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000570 AC: 142AN: 249210Hom.: 0 AF XY: 0.000414 AC XY: 56AN XY: 135196
GnomAD4 exome AF: 0.000227 AC: 332AN: 1461682Hom.: 0 Cov.: 30 AF XY: 0.000193 AC XY: 140AN XY: 727122
GnomAD4 genome ? AF: 0.00192 AC: 292AN: 152262Hom.: 3 Cov.: 32 AF XY: 0.00192 AC XY: 143AN XY: 74434
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 01, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | DNAH11: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at