3-52375363-A-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_015512.5(DNAH1):āc.7109A>Cā(p.Asp2370Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000998 in 1,613,626 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D2370D) has been classified as Likely benign.
Frequency
Consequence
NM_015512.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.7109A>C | p.Asp2370Ala | missense_variant | 45/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.7178A>C | p.Asp2393Ala | missense_variant | 47/80 | ||
DNAH1 | XM_017006130.2 | c.7109A>C | p.Asp2370Ala | missense_variant | 46/79 | ||
DNAH1 | XM_017006131.2 | c.7178A>C | p.Asp2393Ala | missense_variant | 47/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.7109A>C | p.Asp2370Ala | missense_variant | 45/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.7370A>C | non_coding_transcript_exon_variant | 45/77 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000546 AC: 83AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000157 AC: 39AN: 248466Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134826
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461380Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 726936
GnomAD4 genome AF: 0.000545 AC: 83AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000457 AC XY: 34AN XY: 74434
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2022 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at