5-96894046-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022350.5(ERAP2):​c.1126-1200G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,034 control chromosomes in the GnomAD database, including 22,541 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 0.54 ( 22541 hom., cov: 32)

Consequence

ERAP2
NM_022350.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0900
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ERAP2NM_022350.5 linkuse as main transcriptc.1126-1200G>T intron_variant ENST00000437043.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ERAP2ENST00000437043.8 linkuse as main transcriptc.1126-1200G>T intron_variant 1 NM_022350.5 P1Q6P179-1
ENST00000501338.5 linkuse as main transcriptn.1689-20668C>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.544
AC:
82623
AN:
151916
Hom.:
22538
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.570
Gnomad AMI
AF:
0.487
Gnomad AMR
AF:
0.585
Gnomad ASJ
AF:
0.580
Gnomad EAS
AF:
0.555
Gnomad SAS
AF:
0.584
Gnomad FIN
AF:
0.542
Gnomad MID
AF:
0.563
Gnomad NFE
AF:
0.515
Gnomad OTH
AF:
0.539
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.544
AC:
82660
AN:
152034
Hom.:
22541
Cov.:
32
AF XY:
0.546
AC XY:
40583
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.569
Gnomad4 AMR
AF:
0.584
Gnomad4 ASJ
AF:
0.580
Gnomad4 EAS
AF:
0.556
Gnomad4 SAS
AF:
0.585
Gnomad4 FIN
AF:
0.542
Gnomad4 NFE
AF:
0.515
Gnomad4 OTH
AF:
0.535
Alfa
AF:
0.530
Hom.:
2664
Bravo
AF:
0.553
Asia WGS
AF:
0.493
AC:
1717
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
8.8
DANN
Benign
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2247650; hg19: chr5-96229750; API