9-214864-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NR_160804.1(DOCK8-AS1):n.887G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,604,274 control chromosomes in the GnomAD database, including 41,243 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.24 ( 4754 hom., cov: 34)
Exomes 𝑓: 0.22 ( 36489 hom. )
Consequence
DOCK8-AS1
NR_160804.1 non_coding_transcript_exon
NR_160804.1 non_coding_transcript_exon
Scores
15
Clinical Significance
Conservation
PhyloP100: -0.0540
Genes affected
DOCK8-AS1 (HGNC:26436): (DOCK8 antisense RNA 1)
DOCK8 (HGNC:19191): (dedicator of cytokinesis 8) This gene encodes a member of the DOCK180 family of guanine nucleotide exchange factors. Guanine nucleotide exchange factors interact with Rho GTPases and are components of intracellular signaling networks. Mutations in this gene result in the autosomal recessive form of the hyper-IgE syndrome. Alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=6.2680244E-4).
BP6
Variant 9-214864-C-T is Benign according to our data. Variant chr9-214864-C-T is described in ClinVar as [Benign]. Clinvar id is 369626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK8-AS1 | NR_160804.1 | n.887G>A | non_coding_transcript_exon_variant | 1/1 | |||
DOCK8 | NM_203447.4 | upstream_gene_variant | ENST00000432829.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK8-AS1 | ENST00000648587.1 | n.878G>A | non_coding_transcript_exon_variant | 1/1 | |||||
DOCK8 | ENST00000432829.7 | upstream_gene_variant | 1 | NM_203447.4 |
Frequencies
GnomAD3 genomes AF: 0.244 AC: 37095AN: 151916Hom.: 4746 Cov.: 34
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GnomAD3 exomes AF: 0.255 AC: 59015AN: 231510Hom.: 8292 AF XY: 0.253 AC XY: 32375AN XY: 127742
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GnomAD4 exome AF: 0.217 AC: 315097AN: 1452246Hom.: 36489 Cov.: 105 AF XY: 0.220 AC XY: 159020AN XY: 722444
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GnomAD4 genome AF: 0.244 AC: 37138AN: 152028Hom.: 4754 Cov.: 34 AF XY: 0.246 AC XY: 18250AN XY: 74314
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 57% of patients studied by a panel of primary immunodeficiencies. Number of patients: 55. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Hyper-IgE syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
P
PROVEAN
Benign
N
REVEL
Benign
Sift4G
Benign
T
Polyphen
B
Vest4
MPC
ClinPred
T
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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