rs737337
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_020812.4(DOCK6):āc.2136A>Gā(p.Thr712=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,553,570 control chromosomes in the GnomAD database, including 15,801 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.20 ( 4814 hom., cov: 32)
Exomes š: 0.10 ( 10987 hom. )
Consequence
DOCK6
NM_020812.4 synonymous
NM_020812.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.24
Genes affected
DOCK6 (HGNC:19189): (dedicator of cytokinesis 6) This gene encodes a member of the dedicator of cytokinesis (DOCK) family of atypical guanine nucleotide exchange factors. Guanine nucleotide exchange factors interact with small GTPases and are components of intracellular signaling networks. The encoded protein is a group C DOCK protein and plays a role in actin cytoskeletal reorganization by activating the Rho GTPases Cdc42 and Rac1. Mutations in this gene are associated with Adams-Oliver syndrome 2. [provided by RefSeq, Dec 2011]
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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=-0.91).
BP6
?
Variant 19-11236817-T-C is Benign according to our data. Variant chr19-11236817-T-C is described in ClinVar as [Benign]. Clinvar id is 1170730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11236817-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-3.24 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK6 | NM_020812.4 | c.2136A>G | p.Thr712= | synonymous_variant | 19/48 | ENST00000294618.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK6 | ENST00000294618.12 | c.2136A>G | p.Thr712= | synonymous_variant | 19/48 | 1 | NM_020812.4 | A2 | |
DOCK6 | ENST00000587656.6 | c.2136A>G | p.Thr712= | synonymous_variant | 19/49 | 5 | P3 | ||
DOCK6 | ENST00000590680.5 | c.480A>G | p.Thr160= | synonymous_variant | 5/11 | 5 | |||
DOCK6 | ENST00000591750.1 | n.2105A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30275AN: 151990Hom.: 4799 Cov.: 32
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GnomAD3 exomes AF: 0.151 AC: 23987AN: 158802Hom.: 2824 AF XY: 0.141 AC XY: 11908AN XY: 84448
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GnomAD4 exome AF: 0.101 AC: 142035AN: 1401462Hom.: 10987 Cov.: 32 AF XY: 0.102 AC XY: 70294AN XY: 691542
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GnomAD4 genome ? AF: 0.199 AC: 30342AN: 152108Hom.: 4814 Cov.: 32 AF XY: 0.201 AC XY: 14942AN XY: 74378
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 16, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
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