14-34011308-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000487915.6(EGLN3):c.4-80093G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,214 control chromosomes in the GnomAD database, including 1,572 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 0.13 ( 1572 hom., cov: 33)
Consequence
EGLN3
ENST00000487915.6 intron
ENST00000487915.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.720
Publications
6 publications found
Genes affected
EGLN3 (HGNC:14661): (egl-9 family hypoxia inducible factor 3) Enables peptidyl-proline 4-dioxygenase activity. Involved in several processes, including activation of cysteine-type endopeptidase activity involved in apoptotic process; peptidyl-proline hydroxylation to 4-hydroxy-L-proline; and response to hypoxia. Located in cytosol and nucleus. Implicated in renal cell carcinoma. Biomarker of clear cell renal cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC102724945 | XR_001750942.2 | n.484-24146G>A | intron_variant | Intron 5 of 8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGLN3 | ENST00000487915.6 | c.4-80093G>A | intron_variant | Intron 4 of 5 | 5 | ENSP00000451316.1 | ||||
EGLN3 | ENST00000550114.5 | n.55+7293G>A | intron_variant | Intron 1 of 2 | 4 | |||||
EGLN3 | ENST00000551935.5 | n.298-24146G>A | intron_variant | Intron 3 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.132 AC: 20056AN: 152094Hom.: 1572 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
20056
AN:
152094
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.132 AC: 20060AN: 152214Hom.: 1572 Cov.: 33 AF XY: 0.133 AC XY: 9870AN XY: 74418 show subpopulations
GnomAD4 genome
AF:
AC:
20060
AN:
152214
Hom.:
Cov.:
33
AF XY:
AC XY:
9870
AN XY:
74418
show subpopulations
African (AFR)
AF:
AC:
2479
AN:
41544
American (AMR)
AF:
AC:
1347
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
AC:
495
AN:
3464
East Asian (EAS)
AF:
AC:
1550
AN:
5152
South Asian (SAS)
AF:
AC:
732
AN:
4830
European-Finnish (FIN)
AF:
AC:
1568
AN:
10600
Middle Eastern (MID)
AF:
AC:
28
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11387
AN:
68010
Other (OTH)
AF:
AC:
290
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
897
1793
2690
3586
4483
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
709
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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