rs587782293

Positions:

• chr5-112775626-T-A
• chr5-112775626-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PP3 PP5_Very_Strong

The NM_000038.6(APC):​c.423-3T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00018 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: APC NM_000038.6 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.9740
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7 U:1
• Conservation: PhyloP100: 0.613

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 Likely_pathogenic. Variant got 9 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 5-112775626-T-A is Pathogenic according to our data. Variant chr5-112775626-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 142189.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112775626-T-A is described in Lovd as [Likely_pathogenic]. Variant chr5-112775626-T-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APC	NM_000038.6	c.423-3T>A		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.423-3T>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_000038.6	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 149646 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000182 AC: 249 AN: 1365834 Hom.: 0 Cov.: 26 AF XY: 0.000158 AC XY: 108 AN XY: 682286

Gnomad4 AFR exome AF: 0.000466

Gnomad4 AMR exome AF: 0.00265

Gnomad4 ASJ exome AF: 0.000243

Gnomad4 EAS exome AF: 0.0000516

Gnomad4 SAS exome AF: 0.000281

Gnomad4 FIN exome AF: 0.000407

Gnomad4 NFE exome AF: 0.0000690

Gnomad4 OTH exome AF: 0.000177

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 149646 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 72998

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00260 Hom.: 0

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jun 29, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jun 24, 2023	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). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 142189). This variant has been observed in individuals with familial adenomatous polyposis and/or typical or attenuated FAP and individuals undergoing APC testing (PMID: 20223039, 23159591, 33011440; Invitae). It has also been observed to segregate with disease in related individuals. 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 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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Apr 26, 2023	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 20223039, 23159591, 30580288, Myriad internal data]. -

not provided Pathogenic:2 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2022	Published functional studies demonstrate skipping of exon 5 (Rofes 2020); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 28051113, 28152038, 29570743, 20223039, 23159591, 33011440, 30580288) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	May 14, 2024	PS3+PS4_mod -
Uncertain significance, flagged submission	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The APC c.423-3T>A variant was identified in 1 of 2332 proband chromosomes (frequency: 0.0004) from German individuals or families with FAP (Friedl 2005). The variant was identified in the ClinVar database with conflicting classifications. Ambry Genetics classified it as likely pathogenic and the Mayo Clinic Testing Laboratories as of uncertain significance. The InSight Colon Cancer Database identified it 1x with no classification and it was identified in the LOVD database 2x as having splicing effect. The c.423-3T>A variant was not identified in dbSNP, NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) database, Clinvitae database, COSMIC, “Zhejiang Colon Cancer Database”, GeneInsight COGR database, MutDB or UMD. The c.423-3T>A variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% chance of the loss of the splice acceptor site, and 1 of 5 of the above programs predict a greater than 10% chance that this variant alters a cryptic splice donor site. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 20, 2023	The c.423-3T>A intronic pathogenic mutation results from a T to A substitution 3 nucleotides upstream from coding exon 4 in the APC gene. This alteration has been observed in multiple individuals with a personal and/or family history that is consistent with APC-related disease (Friedl W et al. Hered Cancer Clin Pract, 2005 Sep;3:95-114; Kerr SE et al. J Mol Diagn, 2013 Jan;15:31-43; Ambry internal data). This nucleotide position is poorly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Rofes P et al. J Mol Diagn, 2020 12;22:1453-1468; Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 10, 2023	This variant causes a T to A nucleotide substitution at the -3 position of intron 4 of the APC gene. RNA studies report that this variant results in exon 5 skipping predicted to lead to a frameshift truncation (p.Arg141Serfs*8), although the amount of aberrant RNA was not quantified (PMID: 33011440). This variant is highly similar to c.423-3_423-2delAT 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. This variant has been reported in multiple individuals affected with familial adenomatous polyposis (PMID: 20223039, 30580288; External laboratory communication). It has been shown that this variant segregates with disease in multiple members of a family affected by polyposis or colorectal cancer (PMID: 30580288). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	16
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.97
SpliceAI score (max)		0.55		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.55		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs587782293; hg19: chr5-112111323; COSMIC: COSV57327315; COSMIC: COSV57327315;