rs377719435
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001367561.1(DOCK7):c.5724+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,607,320 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 4 hom. )
Consequence
DOCK7
NM_001367561.1 intron
NM_001367561.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.82
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 1-62476049-T-C is Benign according to our data. Variant chr1-62476049-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 445979.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1}.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.000201 (292/1454980) while in subpopulation SAS AF= 0.00246 (211/85778). AF 95% confidence interval is 0.00219. There are 4 homozygotes in gnomad4_exome. There are 194 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK7 | NM_001367561.1 | c.5724+18A>G | intron_variant | ENST00000635253.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK7 | ENST00000635253.2 | c.5724+18A>G | intron_variant | 5 | NM_001367561.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152222Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000371 AC: 92AN: 248130Hom.: 2 AF XY: 0.000492 AC XY: 66AN XY: 134224
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GnomAD4 exome AF: 0.000201 AC: 292AN: 1454980Hom.: 4 Cov.: 29 AF XY: 0.000268 AC XY: 194AN XY: 724262
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GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74506
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 30, 2017 | - - |
Developmental and epileptic encephalopathy, 23 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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