rs6098099
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018431.5(DOK5):c.599+249A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 152,298 control chromosomes in the GnomAD database, including 350 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.064 ( 350 hom., cov: 32)
Consequence
DOK5
NM_018431.5 intron
NM_018431.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.19
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK5 | NM_018431.5 | c.599+249A>C | intron_variant | ENST00000262593.10 | |||
DOK5 | NM_177959.3 | c.275+249A>C | intron_variant | ||||
DOK5 | XM_011528904.2 | c.275+249A>C | intron_variant | ||||
DOK5 | XM_024451946.2 | c.563+249A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK5 | ENST00000262593.10 | c.599+249A>C | intron_variant | 1 | NM_018431.5 | P1 | |||
DOK5 | ENST00000395939.5 | c.275+249A>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0643 AC: 9790AN: 152180Hom.: 350 Cov.: 32
GnomAD3 genomes
?
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152180
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0643 AC: 9789AN: 152298Hom.: 350 Cov.: 32 AF XY: 0.0614 AC XY: 4576AN XY: 74474
GnomAD4 genome
?
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9789
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152298
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32
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4576
AN XY:
74474
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51
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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