rs201631179
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001369.3(DNAH5):c.1645-26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 1,513,890 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.00075 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 4 hom. )
Consequence
DNAH5
NM_001369.3 intron
NM_001369.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.225
Genes affected
DNAH5 (HGNC:2950): (dynein axonemal heavy chain 5) This gene encodes a dynein protein, which is part of a microtubule-associated motor protein complex consisting of heavy, light, and intermediate chains. This protein is an axonemal heavy chain dynein. It functions as a force-generating protein with ATPase activity, whereby the release of ADP is thought to produce the force-producing power stroke. Mutations in this gene cause primary ciliary dyskinesia type 3, as well as Kartagener syndrome, which are both diseases due to ciliary defects. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
This place is a probable branch point but likely benign (scored 2 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 5-13902164-G-A is Benign according to our data. Variant chr5-13902164-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 258005.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.1645-26C>T | intron_variant | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.1645-26C>T | intron_variant | 1 | NM_001369.3 | P4 | |||
DNAH5 | ENST00000681290.1 | c.1600-26C>T | intron_variant | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000749 AC: 114AN: 152186Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000695 AC: 157AN: 225756Hom.: 0 AF XY: 0.000682 AC XY: 83AN XY: 121618
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GnomAD4 exome AF: 0.00138 AC: 1875AN: 1361586Hom.: 4 Cov.: 21 AF XY: 0.00126 AC XY: 859AN XY: 681552
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GnomAD4 genome ? AF: 0.000749 AC: 114AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000604 AC XY: 45AN XY: 74480
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
?
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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