rs7579899

Positions:

• chr2-46310465-A-G
• chr2-46310465-A-T

Variant summary

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

The NM_001430.5(EPAS1):​c.26+12528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,084 control chromosomes in the GnomAD database, including 21,338 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 0.51 (21338 hom., cov: 32)
• Consequence: EPAS1 NM_001430.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

EPAS1 (HGNC:3374): (endothelial PAS domain protein 1) This gene encodes a transcription factor involved in the induction of genes regulated by oxygen, which is induced as oxygen levels fall. The encoded protein contains a basic-helix-loop-helix domain protein dimerization domain as well as a domain found in proteins in signal transduction pathways which respond to oxygen levels. Mutations in this gene are associated with erythrocytosis familial type 4. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPAS1	NM_001430.5	c.26+12528A>G		intron_variant		ENST00000263734.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPAS1	ENST00000263734.5	c.26+12528A>G		intron_variant		1	NM_001430.5	P1
EPAS1	ENST00000449347.5	c.26+12528A>G		intron_variant		3
EPAS1	ENST00000460015.1	n.432+16367A>G		intron_variant, non_coding_transcript_variant		4
EPAS1	ENST00000467888.5	n.174+12528A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78249 AN: 151966 Hom.: 21332 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.515 AC: 78287 AN: 152084 Hom.: 21338 Cov.: 32 AF XY: 0.512 AC XY: 38070 AN XY: 74324

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.534

Alfa AF: 0.571 Hom.: 40556

Bravo AF: 0.508

Asia WGS AF: 0.317 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.66

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: rs7579899; hg19: chr2-46537604;