rs115647631
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The ENST00000420323.7(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
ENST00000420323.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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 | P1 | |
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 | c.1316A>G | p.Lys439Arg | missense_variant, NMD_transcript_variant | 9/20 | 5 | ENSP00000419071 |
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