rs863225354

Positions:

• chr5-112775624-AAT-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2_Supporting PS4_Supporting

This summary comes from the ClinGen Evidence Repository: The c.423-3_423-2del p.(?) variant in APC is an intronic variant which deletes two nucleotides at position -2 and -3 in intron 4. This variant has been reported in 3 probands meeting phenotypic criteria, resulting in a total phenotype score of 1.5 (PS4_Supporting; Ambry Genetics, GeneDX and Invitae internal data). In addition, this variant has also been reported in over 20 individuals with a polyposis phenotype not meeting phenotypic criteria. The results from 2 in silico splicing predictors (VarSEAK and MaxEntScan) indicate that this variant may affect splicing by disrupting the acceptor splice site of intron 4 of APC, but SpliceAI predicts no impact (PP3 not met). This variant is absent from gnomAD v2.1.1 non-cancer dataset (PM2_Supporting). In summary, this variant is a VUS for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PS4_Supporting, PM2_Supporting (VCEP specifications version 1; date of approval 12/12/2022). LINK:https://erepo.genome.network/evrepo/ui/classification/CA038361/MONDO:0021056/089

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: APC NM_000038.6 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Uncertain significance reviewed by expert panel P:5 U:2
• Conservation: PhyloP100: 4.78

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APC	NM_000038.6	c.423-3_423-2del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000257430.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APC	ENST00000257430.9	c.423-3_423-2del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_000038.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000411 AC: 1 AN: 243264 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 131430

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000298

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.99e-7 AC: 1 AN: 1429602 Hom.: 0 AF XY: 0.00000140 AC XY: 1 AN XY: 712290

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.19e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:5 Uncertain:2

Revision: reviewed by expert panel

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:2 Uncertain:1

Uncertain significance, reviewed by expert panel	curation	ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel	Feb 18, 2023	The c.423-3_423-2del p.(?) variant in APC is an intronic variant which deletes two nucleotides at position -2 and -3 in intron 4. This variant has been reported in 3 probands meeting phenotypic criteria, resulting in a total phenotype score of 1.5 (PS4_Supporting; Ambry Genetics, GeneDX and Invitae internal data). In addition, this variant has also been reported in over 20 individuals with a polyposis phenotype not meeting phenotypic criteria. The results from 2 in silico splicing predictors (VarSEAK and MaxEntScan) indicate that this variant may affect splicing by disrupting the acceptor splice site of intron 4 of APC, but SpliceAI predicts no impact (PP3 not met). This variant is absent from gnomAD v2.1.1 non-cancer dataset (PM2_Supporting). In summary, this variant is a VUS for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PS4_Supporting, PM2_Supporting (VCEP specifications version 1; date of approval 12/12/2022). -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	This sequence change falls in intron 4 of the APC gene. It does not directly 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. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has been observed in individuals with clinical features of APC-related conditions (PMID: 20223039, 23159591, 33011440; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 217982). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 5 and introduces a premature termination codon (PMID: 33011440; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 01, 2024	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 06, 2023	This variant deletes two basepairs, c.423-3_423-2del, in the intron 4 acceptor site of the APC gene. This variant is reported to cause abnormal splicing (ClinVar SCV001183798.3) and two similar variants c.423-5_423-3del (synonymous to c.423-4_423-2del) and c.423-3T>A have been reported to cause an estimated 80% to complete out-of-frame skipping of exon 5, respectively (PMID: 25676610, 33011440). This variant is highly similar to c.423-3T>A in terms of the variant acceptor site and its predicted splicing impact, and it may be reported as this alternate cDNA variant description by external laboratories and databases. The variant creates a premature translational stop signal and is expected to result in an absent or non-functional protein product. This variant has been reported in an individual affected with colorectal adenoma (PMID: 33436027) and in individuals with clinical diagnosis of familial adenomatous polyposis, attenuated familial adenomatous polyposis or clinical features of APC-related conditions (ClinVar: SCV000552499.7, SCV001183798.3). Similar variants, c.423-3T>A and c.423-3delT have been reported in multiple individuals affected with familial adenomatous polyposis (PMID: 20223039, 30580288; External laboratory communication (ClinVar: SCV000186122.8, SCV000814096.5)) and c.423-3T>A has been reported to segregate with disease in multiple members of a family affected by polyposis or colorectal cancer (PMID: 30580288). This variant has been identified in 1/243264 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Feb 27, 2024	The c.423-3_423-2delTA intronic pathogenic mutation results from a deletion of two nucleotides at positions c.423-3 and c.423-2 and involves the canonical splice acceptor site before coding exon 4 of the APC gene. Although In silico splice site analysis for this alteration is inconclusive, RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This variant has been observed in multiple individuals with a personal and/or family history that is consistent with APC-associated polyposis conditions (Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Oct 12, 2022

In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23159591, 20223039, 28051113, 28152038) -

not specified Uncertain:1

Uncertain significance, no assertion criteria provided

research

Mayo Clinic Laboratories, Mayo Clinic

-

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.21		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.21		Position offset: 5

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

Publications

LitVar

Other links and lift over

dbSNP: rs863225354; hg19: chr5-112111321;