rs10493326
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001367561.1(DOCK7):c.5494-290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 293,872 control chromosomes in the GnomAD database, including 7,608 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3462 hom., cov: 32)
Exomes 𝑓: 0.23 ( 4146 hom. )
Consequence
DOCK7
NM_001367561.1 intron
NM_001367561.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.74
Genes affected
DOCK7 (HGNC:19190): (dedicator of cytokinesis 7) The protein encoded by this gene is a guanine nucleotide exchange factor (GEF) that plays a role in axon formation and neuronal polarization. The encoded protein displays GEF activity toward RAC1 and RAC3 Rho small GTPases but not toward CDC42. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BP6
?
Variant 1-62487702-G-A is Benign according to our data. Variant chr1-62487702-G-A is described in ClinVar as [Benign]. Clinvar id is 1294572.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK7 | NM_001367561.1 | c.5494-290C>T | intron_variant | ENST00000635253.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK7 | ENST00000635253.2 | c.5494-290C>T | intron_variant | 5 | NM_001367561.1 |
Frequencies
GnomAD3 genomes ? AF: 0.198 AC: 30068AN: 151912Hom.: 3456 Cov.: 32
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GnomAD4 exome AF: 0.231 AC: 32765AN: 141840Hom.: 4146 Cov.: 0 AF XY: 0.229 AC XY: 16756AN XY: 73148
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GnomAD4 genome ? AF: 0.198 AC: 30087AN: 152032Hom.: 3462 Cov.: 32 AF XY: 0.199 AC XY: 14794AN XY: 74300
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 08, 2021 | - - |
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