rs18036

Variant names:

• chr5-96819905-T-C
• rs18036
• ENST00000501338.6:n.1962+3032A>G

Variant summary

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

The ENST00000501338.6(ENSG00000247121):​n.1962+3032A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,142 control chromosomes in the GnomAD database, including 4,184 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 0.23 (4184 hom., cov: 32)
• Consequence: ENSG00000247121 ENST00000501338.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 11 publications found

Genes affected

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERAP1	XM_011543484.3	c.-267+3032A>G		intron_variant	Intron 4 of 23		XP_011541786.1
ERAP1	XM_011543485.3	c.-270-5595A>G		intron_variant	Intron 3 of 22		XP_011541787.1
ERAP1	XM_017009581.2	c.-271+3032A>G		intron_variant	Intron 3 of 22		XP_016865070.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000247121	ENST00000501338.6	n.1962+3032A>G		intron_variant	Intron 3 of 3	2
ENSG00000247121	ENST00000502262.4	n.433+3032A>G		intron_variant	Intron 3 of 3	5
ENSG00000247121	ENST00000504056.5	n.192-5595A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35336 AN: 152024 Hom.: 4179 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.232 AC: 35360 AN: 152142 Hom.: 4184 Cov.: 32 AF XY: 0.232 AC XY: 17268 AN XY: 74364

African (AFR) AF: 0.216 AC: 8952 AN: 41516

American (AMR) AF: 0.196 AC: 2994 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1450 AN: 5172

South Asian (SAS) AF: 0.252 AC: 1212 AN: 4814

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10582

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16711 AN: 67986

Other (OTH) AF: 0.240 AC: 507 AN: 2114

Alfa AF: 0.240 Hom.: 19319

Bravo AF: 0.224

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.68
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs18036; hg19: chr5-96155608;