rs58601841
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The variant allele was found at a frequency of 0.00408 in 741,014 control chromosomes in the GnomAD database, including 82 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 0.014 ( 65 hom., cov: 33)
Exomes 𝑓: 0.0015 ( 17 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.87
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0143 (2165/150934) while in subpopulation AFR AF= 0.049 (2028/41376). AF 95% confidence interval is 0.0472. There are 65 homozygotes in gnomad4. There are 1012 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 61 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.0142 AC: 2142AN: 150826Hom.: 61 Cov.: 33
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GnomAD4 exome AF: 0.00146 AC: 859AN: 590080Hom.: 17 Cov.: 8 AF XY: 0.00134 AC XY: 383AN XY: 284790
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GnomAD4 genome ? AF: 0.0143 AC: 2165AN: 150934Hom.: 65 Cov.: 33 AF XY: 0.0137 AC XY: 1012AN XY: 73750
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at