rs201064587
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015512.5(DNAH1):c.7375G>A(p.Glu2459Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00187 in 1,613,500 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015512.5 missense, splice_region
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.7375G>A | p.Glu2459Lys | missense_variant, splice_region_variant | 47/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.7444G>A | p.Glu2482Lys | missense_variant, splice_region_variant | 49/80 | ||
DNAH1 | XM_017006130.2 | c.7375G>A | p.Glu2459Lys | missense_variant, splice_region_variant | 48/79 | ||
DNAH1 | XM_017006131.2 | c.7444G>A | p.Glu2482Lys | missense_variant, splice_region_variant | 49/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.7375G>A | p.Glu2459Lys | missense_variant, splice_region_variant | 47/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.7636G>A | splice_region_variant, non_coding_transcript_exon_variant | 47/77 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00256 AC: 390AN: 152160Hom.: 3 Cov.: 31
GnomAD3 exomes AF: 0.00256 AC: 638AN: 248786Hom.: 3 AF XY: 0.00249 AC XY: 336AN XY: 134982
GnomAD4 exome AF: 0.00180 AC: 2634AN: 1461222Hom.: 14 Cov.: 31 AF XY: 0.00193 AC XY: 1404AN XY: 726870
GnomAD4 genome ? AF: 0.00256 AC: 390AN: 152278Hom.: 3 Cov.: 31 AF XY: 0.00273 AC XY: 203AN XY: 74452
ClinVar
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | DNAH1: BP4, BS2 - |
DNAH1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at