chrX-46359554-G-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 0.91 ( 32369 hom., 29533 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|
Frequencies
GnomAD3 genomes 0.908 AC: 99999AN: 110153Hom.: 32380 Cov.: 22 AF XY: 0.911 AC XY: 29490AN XY: 32375
GnomAD3 genomes
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110153
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22
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29490
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32375
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.908 AC: 100025AN: 110201Hom.: 32369 Cov.: 22 AF XY: 0.911 AC XY: 29533AN XY: 32433
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
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100025
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110201
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22
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29533
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32433
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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