9-33751017-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000342836.9(PRSS3):c.-53+290C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,066 control chromosomes in the GnomAD database, including 1,358 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (1358 hom., cov: 31)
• Consequence: PRSS3 ENST00000342836.9 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.05

Genes affected

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]

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 9-33751017-C-A is Benign according to our data. Variant chr9-33751017-C-A is described in ClinVar as [Benign]. Clinvar id is 1294450.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE2R2-AS1	NR_170204.1	n.559-12601G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2R2-AS1	ENST00000705030.1	n.644-12601G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16908 AN: 151948 Hom.: 1352 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0667

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.111 AC: 16930 AN: 152066 Hom.: 1358 Cov.: 31 AF XY: 0.111 AC XY: 8244 AN XY: 74334

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.0666

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.0366

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0690

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0325 Hom.: 32

Bravo AF: 0.116

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 15, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs855552; hg19: chr9-33751015;