9-33799372-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRSS3	NM_002771.4	c.*192T>C		downstream_gene_variant		ENST00000379405.4	NP_002762.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRSS3	ENST00000379405.4	c.*192T>C		downstream_gene_variant		1	NM_002771.4	ENSP00000368715.3

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

Gnomad4 AFR exome AF: 0.642

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.617

Gnomad4 EAS exome AF: 0.773

Gnomad4 SAS exome AF: 0.722

Gnomad4 FIN exome AF: 0.677

Gnomad4 NFE exome AF: 0.646

Gnomad4 OTH exome AF: 0.659

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

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.657

Alfa AF: 0.616 Hom.: 58784

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 15, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs216345; hg19: chr9-33799370;