3-52375988-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_015512.5(DNAH1):c.7193G>A(p.Arg2398His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00376 in 1,611,914 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2398C) 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 -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.7193G>A | p.Arg2398His | missense_variant | 46/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.7262G>A | p.Arg2421His | missense_variant | 48/80 | ||
DNAH1 | XM_017006130.2 | c.7193G>A | p.Arg2398His | missense_variant | 47/79 | ||
DNAH1 | XM_017006131.2 | c.7262G>A | p.Arg2421His | missense_variant | 48/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.7193G>A | p.Arg2398His | missense_variant | 46/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.7454G>A | non_coding_transcript_exon_variant | 46/77 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00236 AC: 359AN: 152126Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00207 AC: 511AN: 246984Hom.: 2 AF XY: 0.00218 AC XY: 293AN XY: 134162
GnomAD4 exome AF: 0.00390 AC: 5694AN: 1459670Hom.: 17 Cov.: 31 AF XY: 0.00382 AC XY: 2773AN XY: 726176
GnomAD4 genome AF: 0.00236 AC: 360AN: 152244Hom.: 4 Cov.: 32 AF XY: 0.00218 AC XY: 162AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | DNAH1: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 06, 2023 | - - |
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at