rs200839716
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP3BP6
The NM_001369.3(DNAH5):c.9125G>T(p.Arg3042Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000101 in 1,613,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R3042Q) has been classified as Likely benign.
Frequency
Consequence
NM_001369.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.9125G>T | p.Arg3042Leu | missense_variant | 55/79 | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.9125G>T | p.Arg3042Leu | missense_variant | 55/79 | 1 | NM_001369.3 | P4 | |
DNAH5 | ENST00000681290.1 | c.9080G>T | p.Arg3027Leu | missense_variant | 55/79 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248938Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134638
GnomAD4 exome AF: 0.000106 AC: 155AN: 1461442Hom.: 0 Cov.: 33 AF XY: 0.000102 AC XY: 74AN XY: 727018
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74254
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 14, 2021 | The p.R3042L variant (also known as c.9125G>T), located in coding exon 55 of the DNAH5 gene, results from a G to T substitution at nucleotide position 9125. The arginine at codon 3042 is replaced by leucine, an amino acid with dissimilar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at