5-147828020-A-G

Position:

• chr5-147828020-A-G

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1 PP5

The NM_001379610.1(SPINK1):​c.194+2T>C variant causes a splice donor change. The variant allele was found at a frequency of 0.000114 in 1,609,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00016 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: SPINK1 NM_001379610.1 splice_donor
• Scores: Splicing: ADA: 0.9997
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:14 U:1 O:1
• Conservation: PhyloP100: 4.35

Genes affected

SPINK1 (HGNC:11244): (serine peptidase inhibitor Kazal type 1) The protein encoded by this gene is a trypsin inhibitor, which is secreted from pancreatic acinar cells into pancreatic juice. It is thought to function in the prevention of trypsin-catalyzed premature activation of zymogens within the pancreas and the pancreatic duct. Mutations in this gene are associated with hereditary pancreatitis and tropical calcific pancreatitis. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PP5: Variant 5-147828020-A-G is Pathogenic according to our data. Variant chr5-147828020-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 132142.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, not_provided=1, Uncertain_significance=1, Pathogenic=9}. Variant chr5-147828020-A-G is described in Lovd as [Pathogenic]. Variant chr5-147828020-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPINK1	NM_001379610.1	c.194+2T>C		splice_donor_variant		ENST00000296695.10	NP_001366539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPINK1	ENST00000296695.10	c.194+2T>C		splice_donor_variant		1	NM_001379610.1	ENSP00000296695	P1
SPINK1	ENST00000510027.2	c.196T>C	p.Ter66ArgextTer4	stop_lost	3/3	3		ENSP00000427376
SPINK1	ENST00000505722.1	n.109+2T>C		splice_donor_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.000158 AC: 24 AN: 152208 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000313 AC: 78 AN: 248892 Hom.: 0 AF XY: 0.000253 AC XY: 34 AN XY: 134536

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000291

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00335

Gnomad SAS exome AF: 0.0000660

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000107

Gnomad OTH exome AF: 0.000329

GnomAD4 exome AF: 0.000109 AC: 159 AN: 1456778 Hom.: 0 Cov.: 29 AF XY: 0.000109 AC XY: 79 AN XY: 724932

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00207

Gnomad4 SAS exome AF: 0.000151

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000505

Gnomad4 OTH exome AF: 0.000116

GnomAD4 genome AF: 0.000158 AC: 24 AN: 152326 Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14 AN XY: 74496

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000735

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000390 Hom.: 0

Bravo AF: 0.000212

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000349 AC: 3

ExAC AF: 0.000288 AC: 35

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:14 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary pancreatitis Pathogenic:5 Uncertain:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	This sequence change affects a donor splice site in intron 4 of the SPINK1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs148954387, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individual(s) with chronic pancreatitis (PMID: 15980664, 23017645, 26632706). ClinVar contains an entry for this variant (Variation ID: 132142). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 18978175, 26719302). For these reasons, this variant has been classified as Pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Dec 14, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Human Genetics, Inc, Center for Human Genetics, Inc	Nov 01, 2016	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 13, 2021	The c.194+2T>C intronic pathogenic mutation results from a T to C substitution two nucleotides after coding exon 3 in the SPINK1 gene. This alteration occurs at the 3' terminus of the SPINK1 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 16 amino acids of the protein. The exact functional effect of this alteration is unknown; however, the impacted region is critical for protein function (Ambry internal data). This alteration was first reported in an individual with chronic pancreatitis (Witt H et al. Nat. Genet., 2000 Jun;25:213-6). A functional study found this mutation causes a splicing defect that significantly diminishes SPINK1 expression at the mRNA level and results in diminished trypsin inhibitor secretion (Kereszturi E et al. Gut, 2009 Apr;58:545-9). This mutation has been seen in individuals affected with idiopathic, familial, alcoholic, autoimmune and tropical chronic pancreatitis (Kereszturi E et al. Gut, 2009 Apr;58:545-9; Chang MC et al. J Gastroenterol Hepatol, 2014 Dec;29:2038-42; Cho SM et al. Ann Lab Med, 2016 Nov;36:555-60; Tang XY et al. Dig Liver Dis, 2020 02;52:143-148). This alteration has also been identified in individuals diagnosed with breast and/or pancreatic cancer (Yang X et al. PLoS One, 2015 Apr;10:e0125571; Boortalary T et al. Pancreas, 2018 Apr;47:e24-e25). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 29, 2018	Variant summary: SPINK1 c.194+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. 5/5 computational tools predict a significant impact on normal splicing. These predictions are supported by multiple functional studies, Kume_2006 and Kereszturi_2009, found the variant to significantly affect splicing. Multiple publications have cited the variant in affected individuals diagnosed with chronic pancreatitis, predominantly of Asian origin. Multiple clinical diagnostic laboratories have ClinVar submissions (after 2014) classifying the variant as "pathogenic." GeneReviews, a well-established database, classifies the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:5

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2024	SPINK1: PVS1:Strong, PS4:Moderate, PM2:Supporting, PS3:Supporting -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 13, 2020	The SPINK1 c.194+2T>C variant (rs148954387) has been reported in the literature in numerous individuals diagnosed with chronic pancreatitis (Cho 2016, Kume 2006, Witt 2000, Zou 2018) and is one of the most common pathogenic variants in East Asian individuals affected with pancreatitis (Cho 2016, Zou 2018). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 132142), and it is found in the general population with an overall allele frequency of 0.03% (85/280290 alleles) in the Genome Aggregation Database. This variant abolishes the canonical splice donor site of intron 4, which is likely to disrupt gene function. Indeed, functional studies indicate a significant reduction of mRNA levels, skipping of exon 3, and undetectable levels of the SPINK1 protein (Kereszturi 2009, Kume 2006, Zou 2016). Based on available information, the c.194+2T>C variant is considered to be pathogenic. References: Cho SM et al. PRSS1, SPINK1, CFTR, and CTRC Pathogenic Variants in Korean Patients With Idiopathic Pancreatitis. Ann Lab Med. 2016 Nov;36(6):555-60. Kereszturi E et al. Minigene analysis of intronic variants in common SPINK1 haplotypes associated with chronic pancreatitis. Gut. 2009; 58(4):545-9. Kume K et al. [-215G>A; IVS3+2T>C] mutation in the SPINK1 gene causes exon 3 skipping and loss of the trypsin binding site. Gut. 2006; 55(8):1214. Witt H et al. Mutations in the gene encoding the serine protease inhibitor, Kazal type 1 are associated with chronic pancreatitis. Nat Genet. 2000; 25(2):213-6. Zou WB et al. Clarifying the clinical relevance of SPINK1 intronic variants in chronic pancreatitis. Gut. 2016 May;65(5):884-6. Zou WB et al. SPINK1, PRSS1, CTRC, and CFTR Genotypes Influence Disease Onset and Clinical Outcomes in Chronic Pancreatitis. Clin Transl Gastroenterol. 2018 Nov 12;9(11):204. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 21, 2020	- -

Hereditary pancreatitis;C1842402:Tropical pancreatitis Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Diabetes mellitus Pathogenic:1

Pathogenic, no assertion criteria provided

research

Constantin Polychronakos Laboratory, The Research Institute of the McGill University Health Centre

-

PVS1 PS1 PP2 -

SPINK1-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 20, 2024

The SPINK1 c.194+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported as causative for SPINK1-related disorders, including chronic pancreatitis, and functional studies support its pathogenicity (Witt et al. 2000. PubMed ID: 10835640; Kereszturi et al. 2008. PubMed ID: 18978175; Sun et al. 2015. PubMed ID: 26632706). This variant is reported in 0.33% of alleles in individuals of East Asian descent in gnomAD. Variants that disrupt a consensus splice donor site in SPINK1 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Chronic pancreatitis Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Uncertain	0.11
CADD	Pathogenic	26
DANN	Uncertain	0.99
Eigen	Pathogenic	0.94
Eigen_PC	Pathogenic	0.74
FATHMM_MKL	Uncertain	0.96	D
MutationTaster	Benign	1.0	D;N
GERP RS		4.9

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.34		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.34		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs148954387; hg19: chr5-147207583;