rs200416242
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015512.5(DNAH1):c.10636C>A(p.Arg3546=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000684 in 1,461,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
DNAH1
NM_015512.5 synonymous
NM_015512.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.78
Genes affected
DNAH1 (HGNC:2940): (dynein axonemal heavy chain 1) This gene encodes an inner dynein arm heavy chain that provides structural support between the radial spokes and the outer doublet of the sperm tail. Naturally occurring mutations in this gene are associated with primary ciliary dyskinesia and multiple morphological anomalies of the flagella that result in asthenozoospermia and male infertility. Mice with a homozygous knockout of the orthologous gene are viable but have reduced sperm motility and are infertile. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.14).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.10636C>A | p.Arg3546= | synonymous_variant | 67/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.10705C>A | p.Arg3569= | synonymous_variant | 69/80 | ||
DNAH1 | XM_017006130.2 | c.10636C>A | p.Arg3546= | synonymous_variant | 68/79 | ||
DNAH1 | XM_017006131.2 | c.10579C>A | p.Arg3527= | synonymous_variant | 68/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.10636C>A | p.Arg3546= | synonymous_variant | 67/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.11093C>A | non_coding_transcript_exon_variant | 66/77 | 2 | ||||
DNAH1 | ENST00000488988.5 | n.2422C>A | non_coding_transcript_exon_variant | 14/25 | 2 | ||||
DNAH1 | ENST00000490713.5 | c.1336C>A | p.Arg446= | synonymous_variant, NMD_transcript_variant | 10/20 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248180Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134810
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461586Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727082
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GnomAD4 genome ? Cov.: 32
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?
Cov.:
32
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at