9-33797058-A-T

Variant summary

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

The NM_002771.4(PRSS3):c.200+256A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,994 control chromosomes in the GnomAD database, including 27,079 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.59 (27079 hom., cov: 32)
• Consequence: PRSS3 NM_002771.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0850

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=-0.84).
• BP6: Variant 9-33797058-A-T is Benign according to our data. Variant chr9-33797058-A-T is described in ClinVar as [Benign]. Clinvar id is 1263618.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRSS3	NM_002771.4	c.200+256A>T		intron_variant		ENST00000379405.4
UBE2R2-AS1	NR_170204.1	n.558+1310T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRSS3	ENST00000379405.4	c.200+256A>T		intron_variant		1	NM_002771.4	P1
UBE2R2-AS1	ENST00000705030.1	n.425+1310T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90095 AN: 151876 Hom.: 27076 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.593 AC: 90123 AN: 151994 Hom.: 27079 Cov.: 32 AF XY: 0.592 AC XY: 43988 AN XY: 74298

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.631

Alfa AF: 0.580 Hom.: 3033

Bravo AF: 0.606

Asia WGS AF: 0.650 AC: 2255 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

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.6
Dann	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs83921; hg19: chr9-33797056;