rs200581574
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001277115.2(DNAH11):c.4463C>T(p.Ser1488Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000217 in 1,605,864 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001277115.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 182AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000263 AC: 64AN: 243032Hom.: 0 AF XY: 0.000220 AC XY: 29AN XY: 131660
GnomAD4 exome AF: 0.000115 AC: 167AN: 1453600Hom.: 2 Cov.: 30 AF XY: 0.0000997 AC XY: 72AN XY: 722342
GnomAD4 genome AF: 0.00120 AC: 182AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.00105 AC XY: 78AN XY: 74442
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
- -
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. -
not provided Uncertain:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
DNAH11-related disorder Benign:1
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