9-340229-C-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_203447.4(DOCK8):āc.1587C>Gā(p.Pro529=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000487 in 1,614,102 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P529P) has been classified as Likely benign.
Frequency
Consequence
NM_203447.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK8 | NM_203447.4 | c.1587C>G | p.Pro529= | synonymous_variant | 14/48 | ENST00000432829.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK8 | ENST00000432829.7 | c.1587C>G | p.Pro529= | synonymous_variant | 14/48 | 1 | NM_203447.4 |
Frequencies
GnomAD3 genomes AF: 0.00270 AC: 411AN: 152122Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000752 AC: 189AN: 251300Hom.: 1 AF XY: 0.000501 AC XY: 68AN XY: 135810
GnomAD4 exome AF: 0.000257 AC: 375AN: 1461862Hom.: 3 Cov.: 30 AF XY: 0.000206 AC XY: 150AN XY: 727240
GnomAD4 genome AF: 0.00270 AC: 411AN: 152240Hom.: 1 Cov.: 32 AF XY: 0.00249 AC XY: 185AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | DOCK8: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 07, 2019 | - - |
Autosomal recessive hyper-IgE syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Combined immunodeficiency due to DOCK8 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at