rs1315748049
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015512.5(DNAH1):c.754G>A(p.Asp252Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015512.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.754G>A | p.Asp252Asn | missense_variant | 6/78 | ENST00000420323.7 | NP_056327.4 | |
DNAH1 | XM_017006129.2 | c.754G>A | p.Asp252Asn | missense_variant | 7/80 | XP_016861618.1 | ||
DNAH1 | XM_017006130.2 | c.754G>A | p.Asp252Asn | missense_variant | 7/79 | XP_016861619.1 | ||
DNAH1 | XM_017006131.2 | c.754G>A | p.Asp252Asn | missense_variant | 7/79 | XP_016861620.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.754G>A | p.Asp252Asn | missense_variant | 6/78 | 1 | NM_015512.5 | ENSP00000401514.2 | ||
DNAH1 | ENST00000486752.5 | n.1015G>A | non_coding_transcript_exon_variant | 6/77 | 2 | |||||
DNAH1 | ENST00000497875.1 | n.919G>A | non_coding_transcript_exon_variant | 7/21 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461412Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726944
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 13, 2017 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with DNAH1-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces aspartic acid with asparagine at codon 252 of the DNAH1 protein (p.Asp252Asn). The aspartic acid residue is weakly conserved and there is a small physicochemical difference between aspartic acid and asparagine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at