rs2399153
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 22-17012403-A-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 153,664 control chromosomes in the GnomAD database, including 59,617 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 0.88 ( 59084 hom., cov: 31)
Exomes 𝑓: 0.83 ( 533 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.875
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000605217.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.879 AC: 133659AN: 152032Hom.: 59030 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome AF: 0.830 AC: 1256AN: 1514Hom.: 533 Cov.: 0 AF XY: 0.840 AC XY: 746AN XY: 888
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GnomAD4 genome ? AF: 0.879 AC: 133776AN: 152150Hom.: 59084 Cov.: 31 AF XY: 0.883 AC XY: 65631AN XY: 74362
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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