chr20-54568983-CA-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_018431.5(DOK5):c.174+13965del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.73 ( 25862 hom., cov: 0)
Consequence
DOK5
NM_018431.5 intron
NM_018431.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.131
Genes affected
DOK5 (HGNC:16173): (docking protein 5) The protein encoded by this gene is a member of the DOK family of membrane proteins, which are adapter proteins involved in signal transduction. The encoded protein interacts with phosphorylated receptor tyrosine kinases to mediate neurite outgrowth and activation of the MAP kinase pathway. Unlike other DOK family proteins, this protein does not interact with RASGAP. This protein is up-regulated in patients with systemic sclerosis and is associated with fibrosis induced by insulin-like growth factor binding protein 5. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK5 | NM_018431.5 | c.174+13965del | intron_variant | ENST00000262593.10 | |||
DOK5 | NM_177959.3 | c.-151+13965del | intron_variant | ||||
DOK5 | XM_011528904.2 | c.-151+13965del | intron_variant | ||||
DOK5 | XM_024451946.2 | c.138+13965del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK5 | ENST00000262593.10 | c.174+13965del | intron_variant | 1 | NM_018431.5 | P1 | |||
DOK5 | ENST00000395939.5 | c.-151+13965del | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.731 AC: 70319AN: 96222Hom.: 25887 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.731 AC: 70266AN: 96186Hom.: 25862 Cov.: 0 AF XY: 0.733 AC XY: 32826AN XY: 44758
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ClinVar
Not reported inComputational scores
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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