rs61731638
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015512.5(DNAH1):c.9121C>T(p.Arg3041Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00358 in 1,601,154 control chromosomes in the GnomAD database, including 174 homozygotes. In-silico tool predicts 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. R3041H) 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.9121C>T | p.Arg3041Cys | missense_variant | 57/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.9190C>T | p.Arg3064Cys | missense_variant | 59/80 | ||
DNAH1 | XM_017006130.2 | c.9121C>T | p.Arg3041Cys | missense_variant | 58/79 | ||
DNAH1 | XM_017006131.2 | c.9190C>T | p.Arg3064Cys | missense_variant | 59/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.9121C>T | p.Arg3041Cys | missense_variant | 57/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.9382C>T | non_coding_transcript_exon_variant | 57/77 | 2 | ||||
DNAH1 | ENST00000488988.5 | n.711C>T | non_coding_transcript_exon_variant | 5/25 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0184 AC: 2794AN: 152218Hom.: 74 Cov.: 33
GnomAD3 exomes AF: 0.00460 AC: 1038AN: 225496Hom.: 31 AF XY: 0.00370 AC XY: 452AN XY: 122062
GnomAD4 exome AF: 0.00202 AC: 2933AN: 1448818Hom.: 100 Cov.: 32 AF XY: 0.00177 AC XY: 1270AN XY: 719336
GnomAD4 genome ? AF: 0.0184 AC: 2798AN: 152336Hom.: 74 Cov.: 33 AF XY: 0.0178 AC XY: 1327AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | This variant is associated with the following publications: (PMID: 31213628) - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 16, 2023 | - - |
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