rs9557078
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001366683.2(DOCK9):c.5514+24T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 1,568,862 control chromosomes in the GnomAD database, including 140,170 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 0.41 ( 13458 hom., cov: 32)
Exomes 𝑓: 0.42 ( 126712 hom. )
Consequence
DOCK9
NM_001366683.2 intron
NM_001366683.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0520
Genes affected
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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 (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK9 | NM_001366683.2 | c.5514+24T>G | intron_variant | ENST00000682017.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK9 | ENST00000682017.1 | c.5514+24T>G | intron_variant | NM_001366683.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.413 AC: 62758AN: 151920Hom.: 13446 Cov.: 32
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GnomAD3 exomes AF: 0.420 AC: 102624AN: 244190Hom.: 22659 AF XY: 0.416 AC XY: 55182AN XY: 132494
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GnomAD4 exome AF: 0.417 AC: 591175AN: 1416824Hom.: 126712 Cov.: 30 AF XY: 0.415 AC XY: 290534AN XY: 699722
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GnomAD4 genome ? AF: 0.413 AC: 62813AN: 152038Hom.: 13458 Cov.: 32 AF XY: 0.414 AC XY: 30793AN XY: 74304
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ClinVar
Not reported inComputational scores
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Name
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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