5-13841738-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001369.3(DNAH5):āc.5438A>Gā(p.Glu1813Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. E1813D) has been classified as Uncertain significance.
Frequency
Consequence
NM_001369.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.5438A>G | p.Glu1813Gly | missense_variant | 33/79 | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.5438A>G | p.Glu1813Gly | missense_variant | 33/79 | 1 | NM_001369.3 | P4 | |
DNAH5 | ENST00000681290.1 | c.5393A>G | p.Glu1798Gly | missense_variant | 33/79 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152170Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251248Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135770
GnomAD4 exome AF: 0.000181 AC: 265AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.000154 AC XY: 112AN XY: 727214
GnomAD4 genome AF: 0.000125 AC: 19AN: 152288Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74460
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2016 | The p.E1813G variant (also known as c.5438A>G), located in coding exon 33 of the DNAH5 gene, results from an A to G substitution at nucleotide position 5438. The glutamic acid at codon 1813 is replaced by glycine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at