rs201003363
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_015512.5(DNAH1):āc.2724T>Cā(p.Asn908=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,613,686 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.00097 ( 1 hom., cov: 33)
Exomes š: 0.000078 ( 0 hom. )
Consequence
DNAH1
NM_015512.5 synonymous
NM_015512.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.296
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 Benign. Variant got -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 3-52350585-T-C is Benign according to our data. Variant chr3-52350585-T-C is described in ClinVar as [Benign]. Clinvar id is 544677.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.296 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000965 (147/152300) while in subpopulation AFR AF= 0.00339 (141/41552). AF 95% confidence interval is 0.00294. There are 1 homozygotes in gnomad4. There are 66 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.2724T>C | p.Asn908= | synonymous_variant | 16/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.2724T>C | p.Asn908= | synonymous_variant | 17/80 | ||
DNAH1 | XM_017006130.2 | c.2724T>C | p.Asn908= | synonymous_variant | 17/79 | ||
DNAH1 | XM_017006131.2 | c.2724T>C | p.Asn908= | synonymous_variant | 17/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.2724T>C | p.Asn908= | synonymous_variant | 16/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.2985T>C | non_coding_transcript_exon_variant | 16/77 | 2 | ||||
DNAH1 | ENST00000497875.1 | n.2889T>C | non_coding_transcript_exon_variant | 17/21 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000933 AC: 142AN: 152182Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000193 AC: 48AN: 248424Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134784
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GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461386Hom.: 0 Cov.: 31 AF XY: 0.0000702 AC XY: 51AN XY: 726946
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GnomAD4 genome ? AF: 0.000965 AC: 147AN: 152300Hom.: 1 Cov.: 33 AF XY: 0.000886 AC XY: 66AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at