19-40800316-CT-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000593726.5(EGLN2):c.-246del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 384,246 control chromosomes in the GnomAD database, including 8,838 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 6458 hom., cov: 21)
Exomes 𝑓: 0.22 ( 2380 hom. )
Consequence
EGLN2
ENST00000593726.5 5_prime_UTR
ENST00000593726.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.329
Genes affected
EGLN2 (HGNC:14660): (egl-9 family hypoxia inducible factor 2) The hypoxia inducible factor (HIF) is a transcriptional complex that is involved in oxygen homeostasis. At normal oxygen levels, the alpha subunit of HIF is targeted for degration by prolyl hydroxylation. This gene encodes an enzyme responsible for this post-translational modification. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream RAB4B (RAB4B, member RAS oncogene family) gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 19-40800316-CT-C is Benign according to our data. Variant chr19-40800316-CT-C is described in ClinVar as [Benign]. Clinvar id is 1297762.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGLN2 | NM_080732.4 | c.-234-12del | intron_variant | ENST00000303961.9 | |||
RAB4B-EGLN2 | NR_037791.1 | n.815-12del | intron_variant, non_coding_transcript_variant | ||||
EGLN2 | NM_053046.4 | c.-234-12del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGLN2 | ENST00000303961.9 | c.-234-12del | intron_variant | 1 | NM_080732.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.250 AC: 36990AN: 148046Hom.: 6431 Cov.: 21
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GnomAD4 exome AF: 0.224 AC: 52992AN: 236118Hom.: 2380 Cov.: 0 AF XY: 0.223 AC XY: 27204AN XY: 121910
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GnomAD4 genome ? AF: 0.250 AC: 37059AN: 148128Hom.: 6458 Cov.: 21 AF XY: 0.246 AC XY: 17787AN XY: 72176
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at