rs61734654
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015512.5(DNAH1):c.1789C>T(p.Arg597Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00269 in 1,614,044 control chromosomes in the GnomAD database, including 111 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 Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R597H) has been classified as Uncertain significance.
Frequency
Consequence
NM_015512.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.1789C>T | p.Arg597Cys | missense_variant | 11/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.1789C>T | p.Arg597Cys | missense_variant | 12/80 | ||
DNAH1 | XM_017006130.2 | c.1789C>T | p.Arg597Cys | missense_variant | 12/79 | ||
DNAH1 | XM_017006131.2 | c.1789C>T | p.Arg597Cys | missense_variant | 12/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.1789C>T | p.Arg597Cys | missense_variant | 11/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.2050C>T | non_coding_transcript_exon_variant | 11/77 | 2 | ||||
DNAH1 | ENST00000497875.1 | n.1954C>T | non_coding_transcript_exon_variant | 12/21 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0147 AC: 2244AN: 152222Hom.: 64 Cov.: 33
GnomAD3 exomes AF: 0.00352 AC: 878AN: 249252Hom.: 20 AF XY: 0.00260 AC XY: 352AN XY: 135216
GnomAD4 exome AF: 0.00143 AC: 2094AN: 1461704Hom.: 47 Cov.: 32 AF XY: 0.00117 AC XY: 848AN XY: 727132
GnomAD4 genome ? AF: 0.0148 AC: 2250AN: 152340Hom.: 64 Cov.: 33 AF XY: 0.0142 AC XY: 1061AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 30, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2020 | - - |
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at