rs11714402
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015512.5(DNAH1):āc.3964A>Cā(p.Arg1322=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,579,880 control chromosomes in the GnomAD database, including 24,980 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.18 ( 2849 hom., cov: 32)
Exomes š: 0.17 ( 22131 hom. )
Consequence
DNAH1
NM_015512.5 synonymous
NM_015512.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.257
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 3-52357719-A-C is Benign according to our data. Variant chr3-52357719-A-C is described in ClinVar as [Benign]. Clinvar id is 402598.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.257 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.3964A>C | p.Arg1322= | synonymous_variant | 23/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.3964A>C | p.Arg1322= | synonymous_variant | 24/80 | ||
DNAH1 | XM_017006130.2 | c.3964A>C | p.Arg1322= | synonymous_variant | 24/79 | ||
DNAH1 | XM_017006131.2 | c.3964A>C | p.Arg1322= | synonymous_variant | 24/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.3964A>C | p.Arg1322= | synonymous_variant | 23/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.4225A>C | non_coding_transcript_exon_variant | 23/77 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.183 AC: 27791AN: 152056Hom.: 2845 Cov.: 32
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GnomAD3 exomes AF: 0.139 AC: 27039AN: 194792Hom.: 2125 AF XY: 0.137 AC XY: 14419AN XY: 105158
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GnomAD4 exome AF: 0.171 AC: 243798AN: 1427706Hom.: 22131 Cov.: 33 AF XY: 0.169 AC XY: 119265AN XY: 707098
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GnomAD4 genome ? AF: 0.183 AC: 27811AN: 152174Hom.: 2849 Cov.: 32 AF XY: 0.176 AC XY: 13086AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
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