rs3783457
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 0.0119 in 158,328 control chromosomes in the GnomAD database, including 37 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 0.012 ( 37 hom., cov: 33)
Exomes 𝑓: 0.00033 ( 0 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0170
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0123 (1878/152292) while in subpopulation AFR AF= 0.0426 (1772/41566). AF 95% confidence interval is 0.041. There are 37 homozygotes in gnomad4. There are 905 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 37 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
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Frequencies
GnomAD3 genomes ? AF: 0.0123 AC: 1871AN: 152174Hom.: 37 Cov.: 33
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152174
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33
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GnomAD4 exome AF: 0.000331 AC: 2AN: 6036Hom.: 0 AF XY: 0.000304 AC XY: 1AN XY: 3294
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GnomAD4 genome ? AF: 0.0123 AC: 1878AN: 152292Hom.: 37 Cov.: 33 AF XY: 0.0122 AC XY: 905AN XY: 74456
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1878
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152292
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33
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905
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21
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3478
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