rs2779251
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 0.157 in 398,732 control chromosomes in the GnomAD database, including 5,273 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 0.15 ( 1920 hom., cov: 32)
Exomes 𝑓: 0.16 ( 3353 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.76
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.
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: 0.154 AC: 23418AN: 152128Hom.: 1921 Cov.: 32
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32
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GnomAD3 exomes AF: 0.300 AC: 3AN: 10Hom.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 exome AF: 0.159 AC: 39155AN: 246486Hom.: 3353 Cov.: 0 AF XY: 0.160 AC XY: 19986AN XY: 124942
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GnomAD4 genome ? AF: 0.154 AC: 23422AN: 152246Hom.: 1920 Cov.: 32 AF XY: 0.152 AC XY: 11323AN XY: 74456
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23422
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32
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11323
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281
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
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Prediction
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