rs7579899
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001430.5(EPAS1):c.26+12528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,084 control chromosomes in the GnomAD database, including 21,338 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 0.51 ( 21338 hom., cov: 32)
Consequence
EPAS1
NM_001430.5 intron
NM_001430.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0880
Genes affected
EPAS1 (HGNC:3374): (endothelial PAS domain protein 1) This gene encodes a transcription factor involved in the induction of genes regulated by oxygen, which is induced as oxygen levels fall. The encoded protein contains a basic-helix-loop-helix domain protein dimerization domain as well as a domain found in proteins in signal transduction pathways which respond to oxygen levels. Mutations in this gene are associated with erythrocytosis familial type 4. [provided by RefSeq, Nov 2009]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPAS1 | NM_001430.5 | c.26+12528A>G | intron_variant | ENST00000263734.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPAS1 | ENST00000263734.5 | c.26+12528A>G | intron_variant | 1 | NM_001430.5 | P1 | |||
EPAS1 | ENST00000449347.5 | c.26+12528A>G | intron_variant | 3 | |||||
EPAS1 | ENST00000460015.1 | n.432+16367A>G | intron_variant, non_coding_transcript_variant | 4 | |||||
EPAS1 | ENST00000467888.5 | n.174+12528A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.515 AC: 78249AN: 151966Hom.: 21332 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.515 AC: 78287AN: 152084Hom.: 21338 Cov.: 32 AF XY: 0.512 AC XY: 38070AN XY: 74324
GnomAD4 genome
?
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78287
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32
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38070
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74324
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1106
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3478
ClinVar
Not reported inComputational scores
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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