rs28129

Variant names:

• chr5-96819815-G-A
• rs28129
• XM_011543484.3:c.-267+3122C>T

Variant summary

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

The ENST00000501338.6(ENSG00000247121):​n.1962+3122C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,062 control chromosomes in the GnomAD database, including 33,671 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 (33671 hom., cov: 32)
• Consequence: ENSG00000247121 ENST00000501338.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 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.1962+3122C>T		intron	N/A
	ENSG00000247121	ENST00000502262.4	TSL:5	n.433+3122C>T		intron	N/A
	ENSG00000247121	ENST00000504056.5	TSL:3	n.192-5505C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100350 AN: 151944 Hom.: 33646 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.660 AC: 100436 AN: 152062 Hom.: 33671 Cov.: 32 AF XY: 0.657 AC XY: 48826 AN XY: 74314

African (AFR) AF: 0.606 AC: 25143 AN: 41456

American (AMR) AF: 0.607 AC: 9273 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2387 AN: 5166

South Asian (SAS) AF: 0.559 AC: 2699 AN: 4824

European-Finnish (FIN) AF: 0.727 AC: 7681 AN: 10568

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

European-Non Finnish (NFE) AF: 0.723 AC: 49184 AN: 67990

Other (OTH) AF: 0.651 AC: 1376 AN: 2114

Alfa AF: 0.692 Hom.: 18767

Bravo AF: 0.649

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs28129; hg19: chr5-96155518;