rs479200

chr1-231408034-G-Achr1-231408034-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022051.3(EGLN1):c.891+12964C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,026 control chromosomes in the GnomAD database, including 40,726 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 0.73 (40726 hom., cov: 33)
• Consequence: EGLN1 NM_022051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EGLN1	NM_022051.3	c.891+12964C>T		intron_variant		ENST00000366641.4
EGLN1	NM_001377260.1	c.891+12964C>T		intron_variant
EGLN1	NM_001377261.1	c.891+12964C>T		intron_variant
EGLN1	XM_024447734.2	c.891+12964C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EGLN1	ENST00000366641.4	c.891+12964C>T		intron_variant		1	NM_022051.3	P1

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110804 AN: 151908 Hom.: 40693 Cov.: 33

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.729 AC: 110883 AN: 152026 Hom.: 40726 Cov.: 33 AF XY: 0.726 AC XY: 53962 AN XY: 74284

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.744

Alfa AF: 0.687 Hom.: 2747

Bravo AF: 0.723

Asia WGS AF: 0.621 AC: 2156 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.2
Dann	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs479200; hg19: chr1-231543780;