chr10-127024717-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001290223.2(DOCK1):c.1485G>A(p.Ala495=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00319 in 1,612,312 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0033 ( 15 hom. )
Consequence
DOCK1
NM_001290223.2 synonymous
NM_001290223.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.77
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 10-127024717-G-A is Benign according to our data. Variant chr10-127024717-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640959.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.77 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK1 | NM_001290223.2 | c.1485G>A | p.Ala495= | synonymous_variant | 15/52 | ENST00000623213.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK1 | ENST00000623213.2 | c.1485G>A | p.Ala495= | synonymous_variant | 15/52 | 1 | NM_001290223.2 | ||
ENST00000420941.2 | n.204+1555C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
ENST00000601242.5 | n.151+1555C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00239 AC: 363AN: 152132Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00261 AC: 645AN: 246680Hom.: 2 AF XY: 0.00282 AC XY: 377AN XY: 133642
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GnomAD4 exome AF: 0.00327 AC: 4774AN: 1460062Hom.: 15 Cov.: 30 AF XY: 0.00325 AC XY: 2359AN XY: 726030
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | DOCK1: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at