rs13419896

chr2-46329206-G-A

Variant summary

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

The NM_001430.5(EPAS1):c.27-17667G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,168 control chromosomes in the GnomAD database, including 1,517 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 0.10 (1517 hom., cov: 32)
• Consequence: EPAS1 NM_001430.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

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 (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPAS1	NM_001430.5	c.27-17667G>A		intron_variant		ENST00000263734.5
EPAS1	XM_011532698.3	c.65+3330G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPAS1	ENST00000263734.5	c.27-17667G>A		intron_variant		1	NM_001430.5	P1
EPAS1	ENST00000449347.5	c.27-17667G>A		intron_variant		3
EPAS1	ENST00000460015.1	n.433-17667G>A		intron_variant, non_coding_transcript_variant		4
EPAS1	ENST00000467888.5	n.175-17667G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15438 AN: 152050 Hom.: 1519 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0226

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.102 AC: 15458 AN: 152168 Hom.: 1517 Cov.: 32 AF XY: 0.105 AC XY: 7826 AN XY: 74392

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0595

Gnomad4 NFE AF: 0.0226

Gnomad4 OTH AF: 0.0733

Alfa AF: 0.0505 Hom.: 132

Bravo AF: 0.107

Asia WGS AF: 0.212 AC: 739 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	3.1
Dann	Benign	0.60

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: rs13419896; hg19: chr2-46556345;