rs78940762
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001369.3(DNAH5):c.13126-39G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00235 in 1,606,432 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.012 ( 25 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 45 hom. )
Consequence
DNAH5
NM_001369.3 intron
NM_001369.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.07
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 5-13708374-C-T is Benign according to our data. Variant chr5-13708374-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 257998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0121 (1847/152058) while in subpopulation AFR AF= 0.0415 (1721/41498). AF 95% confidence interval is 0.0398. There are 25 homozygotes in gnomad4. There are 875 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.13126-39G>A | intron_variant | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.13126-39G>A | intron_variant | 1 | NM_001369.3 | P4 | |||
DNAH5 | ENST00000681290.1 | c.13081-39G>A | intron_variant | A1 | |||||
DNAH5 | ENST00000683611.1 | n.459-39G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0121 AC: 1842AN: 151940Hom.: 25 Cov.: 32
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GnomAD3 exomes AF: 0.00327 AC: 817AN: 250088Hom.: 23 AF XY: 0.00240 AC XY: 324AN XY: 135252
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GnomAD4 exome AF: 0.00133 AC: 1932AN: 1454374Hom.: 45 Cov.: 29 AF XY: 0.00111 AC XY: 804AN XY: 724138
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GnomAD4 genome ? AF: 0.0121 AC: 1847AN: 152058Hom.: 25 Cov.: 32 AF XY: 0.0118 AC XY: 875AN XY: 74286
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2019 | - - |
Computational scores
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Name
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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