rs115647631
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_015512.5(DNAH1):āc.10616A>Gā(p.Lys3539Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,614,038 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_015512.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.10616A>G | p.Lys3539Arg | missense_variant | 66/78 | ENST00000420323.7 | NP_056327.4 | |
DNAH1 | XM_017006129.2 | c.10685A>G | p.Lys3562Arg | missense_variant | 68/80 | XP_016861618.1 | ||
DNAH1 | XM_017006130.2 | c.10616A>G | p.Lys3539Arg | missense_variant | 67/79 | XP_016861619.1 | ||
DNAH1 | XM_017006131.2 | c.10559A>G | p.Lys3520Arg | missense_variant | 67/79 | XP_016861620.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.10616A>G | p.Lys3539Arg | missense_variant | 66/78 | 1 | NM_015512.5 | ENSP00000401514.2 | ||
DNAH1 | ENST00000486752.5 | n.11073A>G | non_coding_transcript_exon_variant | 65/77 | 2 | |||||
DNAH1 | ENST00000488988.5 | n.2402A>G | non_coding_transcript_exon_variant | 13/25 | 2 | |||||
DNAH1 | ENST00000490713.5 | n.1316A>G | non_coding_transcript_exon_variant | 9/20 | 5 | ENSP00000419071.1 |
Frequencies
GnomAD3 genomes AF: 0.000920 AC: 140AN: 152242Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000185 AC: 46AN: 249164Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 135202
GnomAD4 exome AF: 0.0000773 AC: 113AN: 1461678Hom.: 1 Cov.: 32 AF XY: 0.0000660 AC XY: 48AN XY: 727124
GnomAD4 genome AF: 0.000919 AC: 140AN: 152360Hom.: 1 Cov.: 32 AF XY: 0.000846 AC XY: 63AN XY: 74506
ClinVar
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 08, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at