Variant 5-96913411-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_022350.5(ERAP2):c.2611C>T(p.Leu871=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 1,613,122 control chromosomes in the GnomAD database, including 219,166 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 ( 22415 hom., cov: 32)

Exomes 𝑓: 0.52 ( 196751 hom. )

Consequence

ERAP2
NM_022350.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.254

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]

ERAP2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-0.254 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERAP2	NM_022350.5 linkuse as main transcript	c.2611C>T	p.Leu871=	synonymous_variant	17/19	ENST00000437043.8	NP_071745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERAP2	ENST00000437043.8 linkuse as main transcript	c.2611C>T	p.Leu871=	synonymous_variant	17/19	1	NM_022350.5	ENSP00000400376	P1	Q6P179-1
	ENST00000501338.5 linkuse as main transcript	n.1688+20711G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82378

AN:

151916

Hom.:

22412

Cov.:

show subpopulations

Gnomad AFR

AF:

0.572

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.579

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.510

Gnomad OTH

AF:

0.541

GnomAD3 exomes

AF:

0.549

AC:

137798

AN:

250984

Hom.:

38131

AF XY:

0.548

AC XY:

74292

AN XY:

135632

show subpopulations

Gnomad AFR exome

AF:

0.575

Gnomad AMR exome

AF:

0.620

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.587

Gnomad SAS exome

AF:

0.575

Gnomad FIN exome

AF:

0.527

Gnomad NFE exome

AF:

0.511

Gnomad OTH exome

AF:

0.540

GnomAD4 exome

AF:

0.517

AC:

755549

AN:

1461086

Hom.:

196751

Cov.:

AF XY:

0.519

AC XY:

377029

AN XY:

726832

show subpopulations

Gnomad4 AFR exome

AF:

0.579

Gnomad4 AMR exome

AF:

0.618

Gnomad4 ASJ exome

AF:

0.601

Gnomad4 EAS exome

AF:

0.535

Gnomad4 SAS exome

AF:

0.587

Gnomad4 FIN exome

AF:

0.525

Gnomad4 NFE exome

AF:

0.502

Gnomad4 OTH exome

AF:

0.521

GnomAD4 genome

AF:

0.542

AC:

82417

AN:

152036

Hom.:

22415

Cov.:

AF XY:

0.545

AC XY:

40462

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.572

Gnomad4 AMR

AF:

0.586

Gnomad4 ASJ

AF:

0.606

Gnomad4 EAS

AF:

0.554

Gnomad4 SAS

AF:

0.580

Gnomad4 FIN

AF:

0.532

Gnomad4 NFE

AF:

0.510

Gnomad4 OTH

AF:

0.536

Alfa

AF:

0.529

Hom.:

27099

Bravo

AF:

0.553

Asia WGS

AF:

0.486

AC:

1691

AN:

3478

EpiCase

AF:

0.517

EpiControl

AF:

0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.0

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over