rs113217588

Variant names:

• chr9-33750455-A-ACACAG
• rs113217588
• ENST00000705030.1:n.644-12044_644-12040dupCTGTG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NR_170201.1(UBE2R2-AS1):​n.370-12044_370-12040dupCTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,541,724 control chromosomes in the GnomAD database, including 105,900 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.43 (15426 hom., cov: 0)
  • Exomes 𝑓: 0.36 (90474 hom.)
• Consequence: UBE2R2-AS1 NR_170201.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.463
• Publications: 1 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 -10 ACMG points.

• BP6: Variant 9-33750455-A-ACACAG is Benign according to our data. Variant chr9-33750455-A-ACACAG is described in ClinVar as Benign. ClinVar VariationId is 1257582.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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.370-12044_370-12040dupCTGTG		intron	N/A
	UBE2R2-AS1	NR_170202.1		n.559-12044_559-12040dupCTGTG		intron	N/A
	UBE2R2-AS1	NR_170203.1		n.560-12044_560-12040dupCTGTG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2R2-AS1	ENST00000705030.1		n.644-12044_644-12040dupCTGTG		intron	N/A
	PRSS3	ENST00000342836.9	TSL:1	c.-325_-324insCACAG		upstream_gene	N/A	ENSP00000340889.5	A0A7P0MNE9
	PRSS3	ENST00000361005.10	TSL:1	c.-557_-556insCACAG		upstream_gene	N/A	ENSP00000354280.6	A0A7P0MP65

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65386 AN: 151492 Hom.: 15390 Cov.: 0

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.355 AC: 493652 AN: 1390114 Hom.: 90474 Cov.: 31 AF XY: 0.352 AC XY: 241681 AN XY: 686048

African (AFR) AF: 0.669 AC: 20920 AN: 31250

American (AMR) AF: 0.348 AC: 12409 AN: 35644

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 9766 AN: 25062

East Asian (EAS) AF: 0.241 AC: 8580 AN: 35658

South Asian (SAS) AF: 0.287 AC: 22652 AN: 78852

European-Finnish (FIN) AF: 0.388 AC: 18863 AN: 48616

Middle Eastern (MID) AF: 0.397 AC: 1610 AN: 4060

European-Non Finnish (NFE) AF: 0.352 AC: 377829 AN: 1073396

Other (OTH) AF: 0.365 AC: 21023 AN: 57576

GnomAD4 genome AF: 0.432 AC: 65479 AN: 151610 Hom.: 15426 Cov.: 0 AF XY: 0.429 AC XY: 31757 AN XY: 74078

African (AFR) AF: 0.644 AC: 26578 AN: 41244

American (AMR) AF: 0.349 AC: 5329 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1368 AN: 3464

East Asian (EAS) AF: 0.261 AC: 1343 AN: 5150

South Asian (SAS) AF: 0.299 AC: 1442 AN: 4826

European-Finnish (FIN) AF: 0.398 AC: 4183 AN: 10510

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23956 AN: 67834

Other (OTH) AF: 0.412 AC: 870 AN: 2110

Alfa AF: 0.414 Hom.: 1472

Bravo AF: 0.442

Asia WGS AF: 0.309 AC: 1073 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
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs113217588; hg19: chr9-33750453;