chr9-33751017-C-A

Variant names:

• chr9-33751017-C-A
• rs855552
• ENST00000342836.9:c.-53+290C>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001197097.3(PRSS3):​c.-47+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 NM_001197097.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.05
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001197097.3. 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
	PRSS3	NM_001197097.3		c.-47+290C>A		intron	N/A	NP_001184026.3	P35030-4
	PRSS3	NM_001197098.1		c.19+165C>A		intron	N/A	NP_001184027.1	P35030
	PRSS3	NM_007343.4		c.-285+290C>A		intron	N/A	NP_031369.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS3	ENST00000342836.9	TSL:1	c.-53+290C>A		intron	N/A	ENSP00000340889.5	A0A7P0MNE9
	PRSS3	ENST00000429677.8	TSL:1	c.19+165C>A		intron	N/A	ENSP00000401828.3	P35030-5
	PRSS3	ENST00000361005.10	TSL:1	c.-285+290C>A		intron	N/A	ENSP00000354280.6	A0A7P0MP65

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

African (AFR) AF: 0.221 AC: 9181 AN: 41450

American (AMR) AF: 0.0666 AC: 1019 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.0366 AC: 188 AN: 5140

South Asian (SAS) AF: 0.142 AC: 685 AN: 4816

European-Finnish (FIN) AF: 0.0526 AC: 558 AN: 10616

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0690 AC: 4687 AN: 67952

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.0408 Hom.: 53

Bravo AF: 0.116

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

ClinVar submissions

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
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.65
PhyloP100		-1.0
PromoterAI		-0.014	Neutral
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: rs855552; hg19: chr9-33751015;