rs2682558
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.185 in 459,756 control chromosomes in the GnomAD database, including 7,584 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 0.19 ( 2078 hom., cov: 27)
Exomes 𝑓: 0.18 ( 5506 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.168
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.
Transcripts
RefSeq
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.190 AC: 24559AN: 129596Hom.: 2080 Cov.: 27
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GnomAD4 exome AF: 0.183 AC: 60443AN: 330048Hom.: 5506 Cov.: 2 AF XY: 0.183 AC XY: 32060AN XY: 175270
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GnomAD4 genome ? AF: 0.189 AC: 24571AN: 129708Hom.: 2078 Cov.: 27 AF XY: 0.187 AC XY: 11798AN XY: 63040
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at