rs2790879

Variant names:

• chr1-231398643-A-C
• rs2790879
• NM_022051.3:c.891+22355T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022051.3(EGLN1):​c.891+22355T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,500 control chromosomes in the GnomAD database, including 27,813 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 0.60 (27813 hom., cov: 32)
• Consequence: EGLN1 NM_022051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 6 publications found

Genes affected

EGLN1 (HGNC:1232): (egl-9 family hypoxia inducible factor 1) The protein encoded by this gene catalyzes the post-translational formation of 4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. HIF is a transcriptional complex that plays a central role in mammalian oxygen homeostasis. This protein functions as a cellular oxygen sensor, and under normal oxygen concentration, modification by prolyl hydroxylation is a key regulatory event that targets HIF subunits for proteasomal destruction via the von Hippel-Lindau ubiquitylation complex. Mutations in this gene are associated with erythrocytosis familial type 3 (ECYT3). [provided by RefSeq, Nov 2009]

EGLN1 Gene-Disease associations (from GenCC):

• erythrocytosis, familial, 3

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• autosomal dominant secondary polycythemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin, high altitude adaptation

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• hereditary pheochromocytoma-paraganglioma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000287856 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EGLN1	NM_022051.3	c.891+22355T>G		intron_variant	Intron 1 of 4	ENST00000366641.4	NP_071334.1
EGLN1	NM_001377260.1	c.891+22355T>G		intron_variant	Intron 1 of 3		NP_001364189.1
EGLN1	NM_001377261.1	c.891+22355T>G		intron_variant	Intron 1 of 3		NP_001364190.1
EGLN1	XM_024447734.2	c.891+22355T>G		intron_variant	Intron 1 of 2		XP_024303502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGLN1	ENST00000366641.4	c.891+22355T>G		intron_variant	Intron 1 of 4	1	NM_022051.3	ENSP00000355601.3
ENSG00000287856	ENST00000662216.1	c.31-24544T>G		intron_variant	Intron 3 of 6			ENSP00000499467.1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91367 AN: 151382 Hom.: 27785 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.604 AC: 91439 AN: 151500 Hom.: 27813 Cov.: 32 AF XY: 0.606 AC XY: 44890 AN XY: 74016

African (AFR) AF: 0.521 AC: 21540 AN: 41330

American (AMR) AF: 0.560 AC: 8519 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2158 AN: 3458

East Asian (EAS) AF: 0.557 AC: 2859 AN: 5136

South Asian (SAS) AF: 0.573 AC: 2759 AN: 4812

European-Finnish (FIN) AF: 0.707 AC: 7411 AN: 10484

Middle Eastern (MID) AF: 0.641 AC: 186 AN: 290

European-Non Finnish (NFE) AF: 0.651 AC: 44117 AN: 67774

Other (OTH) AF: 0.607 AC: 1275 AN: 2102

Alfa AF: 0.624 Hom.: 4310

Bravo AF: 0.590

Asia WGS AF: 0.576 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.42
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2790879; hg19: chr1-231534389; COSMIC: COSV64148642;