Variant rs712300 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000487915.6(EGLN3):c.3+30588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 151,832 control chromosomes in the GnomAD database, including 43,793 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 0.76 ( 43793 hom., cov: 30)

Consequence

EGLN3
ENST00000487915.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.225

Variant links:

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]

EGLN3 links:

EGLN3-AS1 (HGNC:49077): (EGLN3 antisense RNA 1)

EGLN3-AS1 links:

LOC102724945 (HGNC:):

LOC102724945 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EGLN3-AS1	NR_184209.1 link	n.2857G>A		non_coding_transcript_exon_variant	3/3
LOC102724945	XR_001750942.2 link	n.483+30588C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EGLN3	ENST00000487915.6 link	c.3+30588C>T		intron_variant		5		ENSP00000451316.1		G3V3M1
EGLN3	ENST00000551935.5 link	n.297+30588C>T		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.756

AC:

114646

AN:

151714

Hom.:

43745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.804

Gnomad AMI

AF:

0.666

Gnomad AMR

AF:

0.799

Gnomad ASJ

AF:

0.801

Gnomad EAS

AF:

0.996

Gnomad SAS

AF:

0.752

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.820

Gnomad NFE

AF:

0.706

Gnomad OTH

AF:

0.771

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.756

AC:

114755

AN:

151832

Hom.:

43793

Cov.:

AF XY:

0.760

AC XY:

56343

AN XY:

74168

show subpopulations

Gnomad4 AFR

AF:

0.805

Gnomad4 AMR

AF:

0.799

Gnomad4 ASJ

AF:

0.801

Gnomad4 EAS

AF:

0.996

Gnomad4 SAS

AF:

0.752

Gnomad4 FIN

AF:

0.693

Gnomad4 NFE

AF:

0.706

Gnomad4 OTH

AF:

0.773

Alfa

AF:

0.730

Hom.:

11884

Bravo

AF:

0.766

Asia WGS

AF:

0.885

AC:

3075

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.64

DANN

Benign

0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over