9-33750455-A-ACACAG

Variant names:

• chr9-33750455-A-ACACAG
• rs113217588
• ENST00000705030.1:n.644-12040_644-12039insCTGTG

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2R2-AS1	NR_170201.1	n.370-12044_370-12040dupCTGTG		intron_variant	Intron 2 of 3
UBE2R2-AS1	NR_170202.1	n.559-12044_559-12040dupCTGTG		intron_variant	Intron 3 of 4
UBE2R2-AS1	NR_170203.1	n.560-12044_560-12040dupCTGTG		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2R2-AS1	ENST00000705030.1	n.644-12040_644-12039insCTGTG		intron_variant	Intron 4 of 5
PRSS3	ENST00000342836.9	c.-325_-324insCACAG		upstream_gene_variant		1		ENSP00000340889.5
PRSS3	ENST00000361005.10	c.-557_-556insCACAG		upstream_gene_variant		1		ENSP00000354280.6
PRSS3	ENST00000468152.2	n.-224_-223insCACAG		upstream_gene_variant		5

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

Gnomad4 AFR exome AF: 0.669

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.390

Gnomad4 EAS exome AF: 0.241

Gnomad4 SAS exome AF: 0.287

Gnomad4 FIN exome AF: 0.388

Gnomad4 NFE exome AF: 0.352

Gnomad4 OTH exome AF: 0.365

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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.412

Alfa AF: 0.414 Hom.: 1472

Bravo AF: 0.442

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 21, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113217588; hg19: chr9-33750453;