NM_022350.5:c.1504-1292A>T

Variant names:

• chr5-96898829-A-T
• rs3849749
• NM_022350.5:c.1504-1292A>T

Variant summary

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

The NM_022350.5(ERAP2):​c.1504-1292A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,000 control chromosomes in the GnomAD database, including 29,722 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 0.62 (29722 hom., cov: 32)
• Consequence: ERAP2 NM_022350.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 14 publications found

Genes affected

ERAP2 (HGNC:29499): (endoplasmic reticulum aminopeptidase 2) This gene encodes a zinc metalloaminopeptidase of the M1 protease family that resides in the endoplasmic reticulum and functions in N-terminal trimming antigenic epitopes for presentation by major histocompatibility complex (MHC) class I molecules. Certain mutations in this gene are associated with the inflammatory arthritis syndrome ankylosing spondylitis and pre-eclampsia. This gene is located adjacent to a closely related aminopeptidase gene on chromosome 5. [provided by RefSeq, Jul 2016]

ENSG00000247121 (HGNC:):

ERAP1 (HGNC:18173): (endoplasmic reticulum aminopeptidase 1) The protein encoded by this gene is an aminopeptidase involved in trimming HLA class I-binding precursors so that they can be presented on MHC class I molecules. The encoded protein acts as a monomer or as a heterodimer with ERAP2. This protein may also be involved in blood pressure regulation by inactivation of angiotensin II. Three transcript variants encoding two different isoforms have been found for this gene.[provided by RefSeq, Oct 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022350.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERAP2	NM_022350.5	MANE Select	c.1504-1292A>T		intron	N/A	NP_071745.1
	ERAP2	NM_001130140.3		c.1504-1292A>T		intron	N/A	NP_001123612.1
	ERAP2	NM_001437802.1		c.1503+1966A>T		intron	N/A	NP_001424731.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERAP2	ENST00000437043.8	TSL:1 MANE Select	c.1504-1292A>T		intron	N/A	ENSP00000400376.3
	ERAP2	ENST00000379904.8	TSL:1	c.1369-1292A>T		intron	N/A	ENSP00000369235.4
	ERAP2	ENST00000510373.6	TSL:2	c.1504-1292A>T		intron	N/A	ENSP00000421175.2

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94759 AN: 151882 Hom.: 29708 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.624 AC: 94812 AN: 152000 Hom.: 29722 Cov.: 32 AF XY: 0.630 AC XY: 46811 AN XY: 74296

African (AFR) AF: 0.646 AC: 26772 AN: 41420

American (AMR) AF: 0.672 AC: 10281 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3563 AN: 5168

South Asian (SAS) AF: 0.734 AC: 3544 AN: 4830

European-Finnish (FIN) AF: 0.641 AC: 6759 AN: 10548

Middle Eastern (MID) AF: 0.741 AC: 215 AN: 290

European-Non Finnish (NFE) AF: 0.580 AC: 39398 AN: 67966

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.599 Hom.: 3409

Bravo AF: 0.632

Asia WGS AF: 0.638 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.18
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: rs3849749; hg19: chr5-96234533;