XM_011543484.3:c.-450-11399C>T

Variant names:

• chr5-96834519-G-A
• rs845028
• XM_011543484.3:c.-450-11399C>T

Variant summary

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

The XM_011543484.3(ERAP1):​c.-450-11399C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,102 control chromosomes in the GnomAD database, including 39,328 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 0.71 (39328 hom., cov: 32)
• Consequence: ERAP1 XM_011543484.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 10 publications found

Genes affected

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]

ENSG00000247121 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000501338.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000247121	ENST00000501338.6	TSL:2	n.1782-11402C>T		intron	N/A
	ENSG00000247121	ENST00000502262.4	TSL:5	n.253-11402C>T		intron	N/A
	ENSG00000247121	ENST00000504056.5	TSL:3	n.192-20209C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107922 AN: 151984 Hom.: 39305 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.710 AC: 108007 AN: 152102 Hom.: 39328 Cov.: 32 AF XY: 0.711 AC XY: 52876 AN XY: 74340

African (AFR) AF: 0.565 AC: 23425 AN: 41446

American (AMR) AF: 0.708 AC: 10815 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2479 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2856 AN: 5178

South Asian (SAS) AF: 0.702 AC: 3387 AN: 4824

European-Finnish (FIN) AF: 0.807 AC: 8535 AN: 10576

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54066 AN: 68012

Other (OTH) AF: 0.722 AC: 1528 AN: 2116

Alfa AF: 0.762 Hom.: 19358

Bravo AF: 0.693

Asia WGS AF: 0.670 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.092
DANN	Benign	0.37
PhyloP100		-0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs845028; hg19: chr5-96170222;