chr17-11598568-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001372.4(DNAH9):c.70C>G(p.Arg24Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000983 in 1,343,384 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R24Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH9 | NM_001372.4 | c.70C>G | p.Arg24Gly | missense_variant | 1/69 | ENST00000262442.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH9 | ENST00000262442.9 | c.70C>G | p.Arg24Gly | missense_variant | 1/69 | 1 | NM_001372.4 | P1 | |
DNAH9 | ENST00000579406.1 | n.97C>G | non_coding_transcript_exon_variant | 1/8 | 1 | ||||
DNAH9 | ENST00000454412.6 | c.70C>G | p.Arg24Gly | missense_variant | 1/68 | 5 | |||
DNAH9 | ENST00000579828.5 | c.70C>G | p.Arg24Gly | missense_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000274 AC: 4AN: 146056Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000284 AC: 8AN: 28186Hom.: 0 AF XY: 0.000357 AC XY: 6AN XY: 16816
GnomAD4 exome AF: 0.000107 AC: 128AN: 1197328Hom.: 2 Cov.: 32 AF XY: 0.000145 AC XY: 85AN XY: 585708
GnomAD4 genome ? AF: 0.0000274 AC: 4AN: 146056Hom.: 0 Cov.: 31 AF XY: 0.0000422 AC XY: 3AN XY: 71162
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.70C>G (p.R24G) alteration is located in exon 1 (coding exon 1) of the DNAH9 gene. This alteration results from a C to G substitution at nucleotide position 70, causing the arginine (R) at amino acid position 24 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2022 | This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 24 of the DNAH9 protein (p.Arg24Gly). This variant is present in population databases (rs774227660, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with DNAH9-related conditions. ClinVar contains an entry for this variant (Variation ID: 1350370). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at