rs66539932
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The variant allele was found at a frequency of 0.0000774 in 297,084 control chromosomes in the GnomAD database, including 1 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 0.000092 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000062 ( 0 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.984
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
Transcripts
RefSeq
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152230Hom.: 1 Cov.: 33
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GnomAD4 exome AF: 0.0000622 AC: 9AN: 144736Hom.: 0 Cov.: 0 AF XY: 0.0000823 AC XY: 6AN XY: 72936
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GnomAD4 genome AF: 0.0000919 AC: 14AN: 152348Hom.: 1 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74508
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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