5-112835163-C-T

Position:

• chr5-112835163-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2_Supporting PS4_Supporting PS3

This summary comes from the ClinGen Evidence Repository: The c.1956C>T variant in APC is predicted to be a synonymous (silent) variant (p.His652=). It is located at the third-last nucleotide of exon 15. Two RNA based RT-PCR assays demonstrate out-of-frame skipping of exon 15, with evidence that the variant allele produces <10% of the full-length transcript (PS3; PMID:15459959, 22987206). This variant has been reported in 3 probands meeting least 1.5 phenotype points (PS4_Supporting; PMID:15459959, 22987206). The variant is not reported in gnomAD (PM2_supporting). In summary, this variant meets the criteria to be classified as Likely Pathogenic for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PS3, PS4_Supporting and PM2_Supporting (VCEP specifications version 1; date of approval: 12/12/2022). LINK:https://erepo.genome.network/evrepo/ui/classification/CA16618077/MONDO:0021056/089

• Frequency: Genomes: not found (cov: 32)
• Consequence: APC NM_000038.6 splice_region, synonymous
• Scores: Splicing: ADA: 0.9730
• Clinical Significance: Likely pathogenic reviewed by expert panel P:5
• Conservation: PhyloP100: 2.54

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 Likely_pathogenic. Variant got 6 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APC	NM_000038.6	c.1956C>T	p.His652His	splice_region_variant, synonymous_variant	15/16	ENST00000257430.9	NP_000029.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APC	ENST00000257430.9	c.1956C>T	p.His652His	splice_region_variant, synonymous_variant	15/16	5	NM_000038.6	ENSP00000257430.4
ENSG00000258864	ENST00000520401.1	n.228+6191C>T		intron_variant		3		ENSP00000454861.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:5

Revision: reviewed by expert panel

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 27, 2023	This sequence change affects codon 652 of the APC mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the APC protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with familial adenomatous polyposis (FAP) (PMID: 15459959, 22987206; Invitae). ClinVar contains an entry for this variant (Variation ID: 419202). Studies have shown that this variant results in skipping of exon 15 (also called exon 14) and introduces a premature termination codon (PMID: 15459959, 22987206; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, reviewed by expert panel	curation	ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel	Feb 25, 2023	The c.1956C>T variant in APC is predicted to be a synonymous (silent) variant (p.His652=). It is located at the third-last nucleotide of exon 15. Two RNA based RT-PCR assays demonstrate out-of-frame skipping of exon 15, with evidence that the variant allele produces <10% of the full-length transcript (PS3; PMID: 15459959, 22987206). This variant has been reported in 3 probands meeting least 1.5 phenotype points (PS4_Supporting; PMID: 15459959, 22987206). The variant is not reported in gnomAD (PM2_supporting). In summary, this variant meets the criteria to be classified as Likely Pathogenic for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PS3, PS4_Supporting and PM2_Supporting (VCEP specifications version 1; date of approval: 12/12/2022). -

Carcinoma of colon Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The APC p.His652His variant was identified in 2 of 2512 proband chromosomes (frequency: 0.001) from German and Czech individuals or families with FAP/AFAP (Friedl 2005, Schwarzova 2013). Aretz et al (2004) were first to show this silent variant resulted in exon 14 skipping similar to substitutions at highly conserved splice acceptor and donor sites, versus the alternative splicing nature of exon 14 seen in normal controls, which was contrary to calls made by splice prediction models. This finding was also seen by Schwarzova (2013), in a patient with AFAP, who by RNA based RT-PCR analysis was shown to have the same or higher amounts of the mutant transcript in his blood, healthy colon and polyp tissue, compared to the blood and colon mucosa of healthy individuals. The variant was not identified in dbSNP, 1000 Genomes Project, NHLBI GO Exome Sequencing Project , the Exome Aggregation Consortium database, Clinvitae database, Zhejiang Colon Cancer Database (LOVD), ClinVar database, GeneInsight - COGR database, and UMD; but was identified in COSMIC (1x in an adenomacarcinoma of the large intestine, with somatic status) and in InSiGHT Colon Cancer Gene Variant Database (LOVD) (2x as a pathogenic germline mutation, in a classical FAP phenotype, and one unknown phenotype). The c.1956C>T variant occurs in the third last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. Two of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a difference in splicing and functional studies have demonstrated a splicing defect contradicting, increasing the likelihood this variant has clinical significance. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Apr 09, 2018

This variant is denoted APC c.1956C>T at the DNA level. Although the variant is a synonymous substitution at the coding level, preserving a Histidine at codon 652, it has been demonstrated to cause exon skipping by RNA analysis (Aretz 2004, Schwarzová 2013). APC c.1956C>T was not observed in large population cohorts (Lek 2016).This variant has been observed in individuals with classic and attenuated familial adenomatous polyposis and has shown segregation with disease in internal cases, in the literature, and by another clinical laboratory (Aretz 2004, Friedl 2005, Schwarzová 2013, SCV000647207.1). Based on currently available evidence, we consider APC c.1956C>T to be a likely pathogenic variant. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 28, 2021

The c.1956C>T pathogenic variant (also known as p.H652H), located in coding exon 14 of the APC gene, results from a C to T substitution at nucleotide position 1956. This nucleotide substitution does not change the residue at codon 652. This alteration has been reported in multiple individuals with familial adenomatous polyposis (Ambry internal data; Aretz S et al. Hum. Mutat. 2004 Nov;24(5):370-80; Schwarzová L et al. Fam. Cancer 2013 Mar;12(1):35-42). This nucleotide position is highly conserved in available vertebrate species. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis for this alteration is inconclusive. However, multiple RNA analyses have shown that this alteration leads to substantial exon 14 skipping (Ambry internal data; Aretz S et al. 2004; Schwarzová L et al. 2013). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	18
DANN	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.97
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.29		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.29		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: rs1064793716; hg19: chr5-112170860; COSMIC: COSV57389054;