5-96819166-T-C

Variant names:

• chr5-96819166-T-C
• rs34763
• ENST00000501338.6:n.1962+3771A>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+3771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,424 control chromosomes in the GnomAD database, including 33,337 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 0.66 (33337 hom., cov: 31)
• Consequence: ENSG00000247121 ENST00000501338.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERAP1	XM_011543484.3	c.-267+3771A>G		intron_variant	Intron 4 of 23		XP_011541786.1
ERAP1	XM_011543485.3	c.-270-4856A>G		intron_variant	Intron 3 of 22		XP_011541787.1
ERAP1	XM_017009581.2	c.-271+3771A>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+3771A>G		intron_variant	Intron 3 of 3	2
ENSG00000247121	ENST00000502262.4	n.433+3771A>G		intron_variant	Intron 3 of 3	5
ENSG00000247121	ENST00000504056.5	n.192-4856A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99696 AN: 151308 Hom.: 33313 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.659 AC: 99780 AN: 151424 Hom.: 33337 Cov.: 31 AF XY: 0.655 AC XY: 48450 AN XY: 73962

African (AFR) AF: 0.604 AC: 24928 AN: 41238

American (AMR) AF: 0.606 AC: 9236 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1961 AN: 3460

East Asian (EAS) AF: 0.460 AC: 2362 AN: 5136

South Asian (SAS) AF: 0.559 AC: 2692 AN: 4816

European-Finnish (FIN) AF: 0.722 AC: 7562 AN: 10472

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 48965 AN: 67768

Other (OTH) AF: 0.647 AC: 1353 AN: 2092

Alfa AF: 0.691 Hom.: 4447

Bravo AF: 0.648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs34763; hg19: chr5-96154869;