rs2271108
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_024940.8(DOCK5):c.3618C>T(p.Asp1206=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 1,609,664 control chromosomes in the GnomAD database, including 187,713 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.46 ( 16465 hom., cov: 32)
Exomes 𝑓: 0.48 ( 171248 hom. )
Consequence
DOCK5
NM_024940.8 synonymous
NM_024940.8 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.490
Genes affected
DOCK5 (HGNC:23476): (dedicator of cytokinesis 5) This gene encodes a member of the dedicator of cytokinesis protein family. Members of this family act as guanine nucleotide exchange factors for small Rho family G proteins. The protein encoded by this gene is thought to associate with adaptors CRK and CRKL, and function in regulation of intestinal epithelial cell spreading and migration on collagen IV. Similar proteins in mouse and zebrafish also function in myoblast fusion. [provided by RefSeq, Oct 2016]
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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=-0.36).
BP7
?
Synonymous conserved (PhyloP=0.49 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK5 | NM_024940.8 | c.3618C>T | p.Asp1206= | synonymous_variant | 35/52 | ENST00000276440.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK5 | ENST00000276440.12 | c.3618C>T | p.Asp1206= | synonymous_variant | 35/52 | 1 | NM_024940.8 | P1 | |
DOCK5 | ENST00000444569.5 | c.2934C>T | p.Asp978= | synonymous_variant | 27/29 | 5 | |||
DOCK5 | ENST00000467709.6 | c.*1343C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/36 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.462 AC: 70209AN: 151892Hom.: 16454 Cov.: 32
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GnomAD3 exomes AF: 0.474 AC: 117252AN: 247288Hom.: 28397 AF XY: 0.479 AC XY: 64113AN XY: 133770
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GnomAD4 exome AF: 0.483 AC: 703375AN: 1457654Hom.: 171248 Cov.: 44 AF XY: 0.483 AC XY: 350452AN XY: 724936
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GnomAD4 genome ? AF: 0.462 AC: 70246AN: 152010Hom.: 16465 Cov.: 32 AF XY: 0.468 AC XY: 34791AN XY: 74308
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ClinVar
Not reported inComputational scores
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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