rs4426448
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_152721.6(DOK6):āc.438A>Gā(p.Thr146=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 1,612,720 control chromosomes in the GnomAD database, including 176,726 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: š 0.46 ( 16419 hom., cov: 32)
Exomes š: 0.47 ( 160307 hom. )
Consequence
DOK6
NM_152721.6 synonymous
NM_152721.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.795
Genes affected
DOK6 (HGNC:28301): (docking protein 6) DOK6 is a member of the DOK (see DOK1; MIM 602919) family of intracellular adaptors that play a role in the RET (MIM 164761) signaling cascade (Crowder et al., 2004 [PubMed 15286081]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
?
Synonymous conserved (PhyloP=-0.795 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK6 | NM_152721.6 | c.438A>G | p.Thr146= | synonymous_variant | 5/8 | ENST00000382713.10 | |
DOK6 | XM_017025610.2 | c.114A>G | p.Thr38= | synonymous_variant | 3/6 | ||
DOK6 | XM_017025611.2 | c.114A>G | p.Thr38= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK6 | ENST00000382713.10 | c.438A>G | p.Thr146= | synonymous_variant | 5/8 | 1 | NM_152721.6 | P1 | |
DOK6 | ENST00000582992.1 | c.150A>G | p.Thr50= | synonymous_variant | 2/3 | 3 | |||
DOK6 | ENST00000582172.5 | n.409A>G | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
DOK6 | ENST00000584435.1 | n.252A>G | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.460 AC: 69844AN: 151964Hom.: 16415 Cov.: 32
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GnomAD3 exomes AF: 0.464 AC: 116000AN: 250210Hom.: 28065 AF XY: 0.463 AC XY: 62659AN XY: 135250
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GnomAD4 exome AF: 0.466 AC: 680077AN: 1460638Hom.: 160307 Cov.: 42 AF XY: 0.464 AC XY: 337254AN XY: 726648
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GnomAD4 genome ? AF: 0.459 AC: 69878AN: 152082Hom.: 16419 Cov.: 32 AF XY: 0.459 AC XY: 34130AN XY: 74342
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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