rs2296636
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001290223.2(DOCK1):c.3284-15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,594,248 control chromosomes in the GnomAD database, including 54,328 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 0.23 ( 4156 hom., cov: 33)
Exomes 𝑓: 0.26 ( 50172 hom. )
Consequence
DOCK1
NM_001290223.2 intron
NM_001290223.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.967
Genes affected
DOCK1 (HGNC:2987): (dedicator of cytokinesis 1) This gene encodes a member of the dedicator of cytokinesis protein family. Dedicator of cytokinesis proteins act as guanine nucleotide exchange factors for small Rho family G proteins. The encoded protein regulates the small GTPase Rac, thereby influencing several biological processes, including phagocytosis and cell migration. Overexpression of this gene has also been associated with certain cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 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 (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DOCK1 | ENST00000623213.2 | c.3284-15C>T | intron_variant | 1 | NM_001290223.2 | ENSP00000485033.1 | ||||
DOCK1 | ENST00000280333.9 | c.3221-15C>T | intron_variant | 1 | ENSP00000280333.6 |
Frequencies
GnomAD3 genomes AF: 0.232 AC: 35188AN: 151996Hom.: 4148 Cov.: 33
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GnomAD3 exomes AF: 0.232 AC: 53825AN: 231856Hom.: 6531 AF XY: 0.239 AC XY: 30058AN XY: 125688
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GnomAD4 exome AF: 0.261 AC: 376501AN: 1442134Hom.: 50172 Cov.: 31 AF XY: 0.262 AC XY: 187389AN XY: 716276
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GnomAD4 genome AF: 0.232 AC: 35215AN: 152114Hom.: 4156 Cov.: 33 AF XY: 0.232 AC XY: 17285AN XY: 74348
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at