rs1981846

Variant names:

• chr5-96933158-C-A
• rs1981846
• ENST00000501338.6:n.1688+964G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-96933158-C-A
• chr5-96933158-C-T

Variant summary

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

The ENST00000501338.6(ENSG00000247121):​n.1688+964G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 150,100 control chromosomes in the GnomAD database, including 18,728 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 0.50 (18728 hom., cov: 28)
• Consequence: ENSG00000247121 ENST00000501338.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 16 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=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERAP1	XM_011543484.3	c.-702+964G>T		intron_variant	Intron 1 of 23		XP_011541786.1
ERAP1	XM_011543485.3	c.-522+964G>T		intron_variant	Intron 1 of 22		XP_011541787.1
ERAP1	XM_017009581.2	c.-548+964G>T		intron_variant	Intron 1 of 22		XP_016865070.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000247121	ENST00000501338.6	n.1688+964G>T		intron_variant	Intron 1 of 3	2
ENSG00000247121	ENST00000655392.1	n.818+964G>T		intron_variant	Intron 1 of 3
ENSG00000247121	ENST00000656950.1	n.834+964G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.497 AC: 74539 AN: 149996 Hom.: 18685 Cov.: 28

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.497 AC: 74643 AN: 150100 Hom.: 18728 Cov.: 28 AF XY: 0.494 AC XY: 36126 AN XY: 73122

African (AFR) AF: 0.565 AC: 22953 AN: 40658

American (AMR) AF: 0.427 AC: 6435 AN: 15078

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1371 AN: 3464

East Asian (EAS) AF: 0.442 AC: 2268 AN: 5128

South Asian (SAS) AF: 0.438 AC: 2092 AN: 4776

European-Finnish (FIN) AF: 0.466 AC: 4621 AN: 9908

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33297 AN: 67806

Other (OTH) AF: 0.488 AC: 1017 AN: 2086

Alfa AF: 0.480 Hom.: 9099

Bravo AF: 0.494

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.8
DANN	Benign	0.62
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1981846; hg19: chr5-96268862;