rs12429249
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001366683.2(DOCK9):c.334-46G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,454,830 control chromosomes in the GnomAD database, including 22,546 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 0.15 ( 1971 hom., cov: 33)
Exomes 𝑓: 0.18 ( 20575 hom. )
Consequence
DOCK9
NM_001366683.2 intron
NM_001366683.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.33
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=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK9 | NM_001366683.2 | c.334-46G>A | intron_variant | ENST00000682017.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK9 | ENST00000682017.1 | c.334-46G>A | intron_variant | NM_001366683.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.153 AC: 23261AN: 152048Hom.: 1970 Cov.: 33
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GnomAD3 exomes AF: 0.188 AC: 23839AN: 126960Hom.: 2323 AF XY: 0.186 AC XY: 12606AN XY: 67662
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GnomAD4 exome AF: 0.176 AC: 228739AN: 1302662Hom.: 20575 Cov.: 19 AF XY: 0.176 AC XY: 113674AN XY: 644156
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GnomAD4 genome ? AF: 0.153 AC: 23270AN: 152168Hom.: 1971 Cov.: 33 AF XY: 0.153 AC XY: 11415AN XY: 74386
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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