rs2712381

Variant names:

• chr3-128619757-A-C
• rs2712381
• ENST00000818792.1:n.516-750A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-128619757-A-C
• chr3-128619757-A-G
• chr3-128619757-A-T

Variant summary

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

The ENST00000818792.1(ENSG00000306468):​n.516-750A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,968 control chromosomes in the GnomAD database, including 28,765 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 0.61 (28765 hom., cov: 32)
• Consequence: ENSG00000306468 ENST00000818792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 27 publications found

Genes affected

ENSG00000306468 (HGNC:):

RPN1 (HGNC:10381): (ribophorin I) This gene encodes a type I integral membrane protein found only in the rough endoplasmic reticulum. The encoded protein is part of an N-oligosaccharyl transferase complex that links high mannose oligosaccharides to asparagine residues found in the Asn-X-Ser/Thr consensus motif of nascent polypeptide chains. This protein forms part of the regulatory subunit of the 26S proteasome and may mediate binding of ubiquitin-like domains to this proteasome. [provided by RefSeq, Jul 2008]

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 (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPN1	NM_002950.4	c.*654T>G		downstream_gene_variant		ENST00000296255.8	NP_002941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPN1	ENST00000296255.8	c.*654T>G		downstream_gene_variant		1	NM_002950.4	ENSP00000296255.3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93180 AN: 151850 Hom.: 28723 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.614 AC: 93272 AN: 151968 Hom.: 28765 Cov.: 32 AF XY: 0.614 AC XY: 45577 AN XY: 74274

African (AFR) AF: 0.608 AC: 25177 AN: 41418

American (AMR) AF: 0.591 AC: 9016 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2102 AN: 3470

East Asian (EAS) AF: 0.768 AC: 3973 AN: 5172

South Asian (SAS) AF: 0.555 AC: 2682 AN: 4830

European-Finnish (FIN) AF: 0.618 AC: 6522 AN: 10546

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41743 AN: 67960

Other (OTH) AF: 0.623 AC: 1313 AN: 2108

Alfa AF: 0.613 Hom.: 65689

Bravo AF: 0.613

Asia WGS AF: 0.676 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.038
DANN	Benign	0.69
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2712381; hg19: chr3-128338600;