rs587783035

Positions:

• chr5-112834949-A-G
• chr5-112834949-A-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000038.6(APC):​c.1744-2A>G variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: APC NM_000038.6 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 8.95

Genes affected

APC (HGNC:583): (APC regulator of WNT signaling pathway) This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. It is also involved in other processes including cell migration and adhesion, transcriptional activation, and apoptosis. Defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Mutations in the APC gene have been found to occur in most colorectal cancers, where disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. [provided by RefSeq, Jun 2022]

ENSG00000258864 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 4.1, offset of -26, new splice context is: caaattccaactctaattAGatg. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 5-112834949-A-G is Pathogenic according to our data. Variant chr5-112834949-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 156482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112834949-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APC	NM_000038.6	c.1744-2A>G		splice_acceptor_variant, intron_variant		ENST00000257430.9	NP_000029.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APC	ENST00000257430.9	c.1744-2A>G		splice_acceptor_variant, intron_variant		5	NM_000038.6	ENSP00000257430.4
ENSG00000258864	ENST00000520401.1	n.228+5977A>G		intron_variant		3		ENSP00000454861.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 09, 2023	For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in skipping of exon 15 and introduces a new termination codon (PMID: 9298819, 15459959). However the mRNA is not expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 156482). Disruption of this splice site has been observed in individuals with familial adenomatous polyposis (FAP) (PMID: 8990002, 9298819, 11247896, 15459959, 20223039, 20564245). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 14 of the APC gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely disrupts the C-terminus of the protein. -
Pathogenic, no assertion criteria provided	clinical testing	Pathway Genomics	Jul 24, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	May 03, 2023	This variant is considered pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 15459959]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 10713886]. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	May 02, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 26, 2023	The APC c.1744-2A>G variant disrupts a canonical splice-acceptor site and interferes with normal APC mRNA splicing. This variant has been reported in the published literature in individuals and families with familial adenomatous polyposis (FAP) (PMIDs: 23159591 (2013), 21315632 (2011), 20564245 (2010), 20223039 (2005), 15459959 (2004), 11247896 (2001), 10713886 (2000), 8990002 (1997), 9298819 (1997)). An experimental study reports the skipping of exon 14 due to improper splicing is damaging to APC protein function (PMID: 9298819 (1997)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 07, 2019	This variant causes an A>G nucleotide substitution at the -2 position of intron 14 of the APC gene. Functional RNA studies have shown that this variant causes skipping of exon 15 (also reported as exon 14 in the literature) and this mutant transcript is expected to create a frameshift and a premature translation stop signal and be expressed as a truncated protein (PMID: 9298819, 15459959). Analysis of lymphoblastoid B cells from individuals carrying this variant has demonstrated the expression of the low-molecular-weight APC protein encoded by this mutant transcript (PMID: 9298819). This variant has been reported in more than 10 individuals affected with familial adenomatous polyposis (PMID: 8990002, 9298819, 10713886, 11247896, 15459959, 20223039, 20564245, 23159591). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of APC function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 03, 2019	The c.1744-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides upstream from coding exon 14 in the APC gene. This alteration has been seen in multiple unrelated families with personal and/or family history consistent with familial adenomatous polyposis and has been demonstrated to result in an RNA transcript that skips coding exon 14 (Ambry internal data; van der Luijt RB et al. Hum. Mutat. 1997;9:7-16; Bala S et al. Hum. Mutat., 1997;10:201-6; Aretz S et al. Hum. Mutat. 2004 Nov;24:370-80; Friedl W et al. Hered Cancer Clin Pract, 2005 Sep;3:95-114; Miclea RL et al. J. Bone Miner. Res., 2010 Dec;25:2624-32; Kerr SE et al. J Mol Diagn, 2013 Jan;15:31-43). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. As such, this alteration is classified as a disease-causing mutation. -

Familial multiple polyposis syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Aug 23, 2022

Variant summary: APC c.1744-2A>G 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. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a canonical 3' splice acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing resulting in skipping of exon 14 (example, Bala_1997). The variant was absent in 251084 control chromosomes. c.1744-2A>G has been reported in the literature in multiple individuals affected with Familial Adenomatous Polyposis (example, Aretz_2004, Cao_2000, Lima_2011, Miclea_2010, Kim_2019). These data indicate that the variant is very likely to be associated with disease. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Carcinoma of colon Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The APC c.1744-2A>G variant was identified in 2 of 2542 proband chromosomes (frequency: 0.001) from individuals or families with FAP (van der Luijt 1997, Friedl 2005, Friedl 2001, Aretz 2004). RNA based analysis showed that the variant caused exon 14 skipping by abolishing the consensus splice site, correlating with in silico prediction models (Aretz 2004). The variant was identified in the HGMD, InSiGHT Colon Cancer Gene Variant Database (3X), and the ClinVar database (classified as a Pathogenic variant by Pathway Genomics). The c.1744-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.32
CADD	Pathogenic	28
DANN	Uncertain	0.99
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.1
FATHMM_MKL	Pathogenic	0.99	D
GERP RS		5.9

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.97		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.97		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: rs587783035; hg19: chr5-112170646; COSMIC: COSV57388372; COSMIC: COSV57388372;