16-3889456-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
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 0.0093 ( 0 hom., cov: 3)
Failed GnomAD Quality Control
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.167
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| use as main transcript | n.3889456C>T | intergenic_region |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|
Frequencies
GnomAD3 genomes 0.00 AC: 85AN: 9102Hom.: 0 Cov.: 3 FAILED QC
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00933 AC: 85AN: 9108Hom.: 0 Cov.: 3 AF XY: 0.00887 AC XY: 35AN XY: 3948
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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35
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3948
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at