rs216345

Variant names:

• chr9-33799372-T-C
• rs216345
• ENST00000454429.2:n.296+415A>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_170201.1(UBE2R2-AS1):​n.369+415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 577,094 control chromosomes in the GnomAD database, including 121,044 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.66 (29270 hom., cov: 33)
  • Exomes 𝑓: 0.66 (91774 hom.)
• Consequence: UBE2R2-AS1 NR_170201.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.85
• Publications: 26 publications found

Genes affected

UBE2R2-AS1 (HGNC:49911): (UBE2R2 antisense RNA 1)

PRSS3 (HGNC:9486): (serine protease 3) This gene encodes a trypsinogen, which is a member of the trypsin family of serine proteases. This enzyme is expressed in the brain and pancreas and is resistant to common trypsin inhibitors. It is active on peptide linkages involving the carboxyl group of lysine or arginine. This gene is localized to the locus of T cell receptor beta variable orphans on chromosome 9. Four transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2010]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 9-33799372-T-C is Benign according to our data. Variant chr9-33799372-T-C is described in ClinVar as Benign. ClinVar VariationId is 1246185.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_170201.1. 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
	UBE2R2-AS1	NR_170201.1		n.369+415A>G		intron	N/A
	UBE2R2-AS1	NR_170202.1		n.373+411A>G		intron	N/A
	UBE2R2-AS1	NR_170203.1		n.369+415A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2R2-AS1	ENST00000454429.2	TSL:5	n.296+415A>G		intron	N/A
	UBE2R2-AS1	ENST00000668091.1		n.1295+415A>G		intron	N/A
	UBE2R2-AS1	ENST00000669609.1		n.1400+415A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.656 AC: 94317 AN: 143682 Hom.: 29238 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.578

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.657

GnomAD4 exome AF: 0.665 AC: 287962 AN: 433292 Hom.: 91774 AF XY: 0.665 AC XY: 148804 AN XY: 223738

African (AFR) AF: 0.642 AC: 7573 AN: 11792

American (AMR) AF: 0.685 AC: 11522 AN: 16816

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 7132 AN: 11566

East Asian (EAS) AF: 0.773 AC: 23345 AN: 30186

South Asian (SAS) AF: 0.722 AC: 22767 AN: 31550

European-Finnish (FIN) AF: 0.677 AC: 25522 AN: 37702

Middle Eastern (MID) AF: 0.651 AC: 1272 AN: 1954

European-Non Finnish (NFE) AF: 0.646 AC: 173072 AN: 267808

Other (OTH) AF: 0.659 AC: 15757 AN: 23918

GnomAD4 genome AF: 0.656 AC: 94403 AN: 143802 Hom.: 29270 Cov.: 33 AF XY: 0.660 AC XY: 46347 AN XY: 70270

African (AFR) AF: 0.640 AC: 24533 AN: 38318

American (AMR) AF: 0.689 AC: 10105 AN: 14666

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 1946 AN: 3240

East Asian (EAS) AF: 0.741 AC: 3801 AN: 5128

South Asian (SAS) AF: 0.710 AC: 3344 AN: 4710

European-Finnish (FIN) AF: 0.662 AC: 6651 AN: 10050

Middle Eastern (MID) AF: 0.554 AC: 153 AN: 276

European-Non Finnish (NFE) AF: 0.651 AC: 42018 AN: 64584

Other (OTH) AF: 0.657 AC: 1292 AN: 1968

Alfa AF: 0.615 Hom.: 96473

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.60
PhyloP100		-2.8
Mutation Taster		=61/39	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs216345; hg19: chr9-33799370;