rs10275038
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001363540.2(DOCK4):c.2601+29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,608,382 control chromosomes in the GnomAD database, including 58,457 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 0.38 ( 16028 hom., cov: 32)
Exomes 𝑓: 0.22 ( 42429 hom. )
Consequence
DOCK4
NM_001363540.2 intron
NM_001363540.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.342
Genes affected
DOCK4 (HGNC:19192): (dedicator of cytokinesis 4) This gene is a member of the dedicator of cytokinesis (DOCK) family and encodes a protein with a DHR-1 (CZH-1) domain, a DHR-2 (CZH-2) domain and an SH3 domain. This membrane-associated, cytoplasmic protein functions as a guanine nucleotide exchange factor and is involved in regulation of adherens junctions between cells. Mutations in this gene have been associated with ovarian, prostate, glioma, and colorectal cancers. Alternatively spliced variants which encode different protein isoforms have been described, but only one has been fully characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK4 | NM_001363540.2 | c.2601+29C>T | intron_variant | ENST00000428084.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK4 | ENST00000428084.6 | c.2601+29C>T | intron_variant | 5 | NM_001363540.2 | P3 | |||
DOCK4 | ENST00000423057.6 | c.956+29C>T | intron_variant | 1 | |||||
DOCK4 | ENST00000437633.6 | c.2601+29C>T | intron_variant | 1 | A1 | ||||
DOCK4 | ENST00000445943.5 | c.2564+29C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.375 AC: 56938AN: 151984Hom.: 15977 Cov.: 32
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GnomAD3 exomes AF: 0.248 AC: 61348AN: 247768Hom.: 10331 AF XY: 0.238 AC XY: 31974AN XY: 134356
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GnomAD4 exome AF: 0.221 AC: 322080AN: 1456280Hom.: 42429 Cov.: 30 AF XY: 0.219 AC XY: 158478AN XY: 724296
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GnomAD4 genome ? AF: 0.375 AC: 57051AN: 152102Hom.: 16028 Cov.: 32 AF XY: 0.368 AC XY: 27362AN XY: 74352
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at