rs116172511
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001367561.1(DOCK7):āc.1392A>Gā(p.Pro464=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000958 in 1,614,036 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0052 ( 8 hom., cov: 32)
Exomes š: 0.00051 ( 4 hom. )
Consequence
DOCK7
NM_001367561.1 synonymous
NM_001367561.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.669
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 1-62625292-T-C is Benign according to our data. Variant chr1-62625292-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 475126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.669 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00524 (798/152294) while in subpopulation AFR AF= 0.0182 (757/41566). AF 95% confidence interval is 0.0171. There are 8 homozygotes in gnomad4. There are 356 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK7 | NM_001367561.1 | c.1392A>G | p.Pro464= | synonymous_variant | 12/50 | ENST00000635253.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK7 | ENST00000635253.2 | c.1392A>G | p.Pro464= | synonymous_variant | 12/50 | 5 | NM_001367561.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00525 AC: 799AN: 152176Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00150 AC: 378AN: 251420Hom.: 3 AF XY: 0.000971 AC XY: 132AN XY: 135874
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GnomAD4 exome AF: 0.000512 AC: 749AN: 1461742Hom.: 4 Cov.: 31 AF XY: 0.000435 AC XY: 316AN XY: 727170
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GnomAD4 genome ? AF: 0.00524 AC: 798AN: 152294Hom.: 8 Cov.: 32 AF XY: 0.00478 AC XY: 356AN XY: 74454
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy, 23 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 08, 2019 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 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