rs2468680
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 8-139508977-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,116 control chromosomes in the GnomAD database, including 6,966 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 0.29 ( 6963 hom., cov: 33)
Exomes 𝑓: 0.38 ( 3 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.38
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=-1.05).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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 |
---|---|---|---|---|---|---|---|---|---|
ENST00000611315.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.290 AC: 44109AN: 151974Hom.: 6956 Cov.: 33
GnomAD3 genomes
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44109
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151974
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33
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GnomAD4 exome AF: 0.375 AC: 9AN: 24Hom.: 3 Cov.: 0 AF XY: 0.563 AC XY: 9AN XY: 16
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GnomAD4 genome ? AF: 0.290 AC: 44141AN: 152092Hom.: 6963 Cov.: 33 AF XY: 0.299 AC XY: 22236AN XY: 74330
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44141
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33
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22236
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74330
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Asia WGS
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1580
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3478
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