NM_000038.6:c.1626+3A>G

Variant names:

• chr5-112828009-A-G
• rs1060503372
• NM_000038.6:c.1626+3A>G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PS4_Moderate PP3 PM2_Supporting PS3_Moderate

This summary comes from the ClinGen Evidence Repository: The c.1626+3A>G variant in APC is an intronic variant which is located at the 3rd nucleotide in intron 13. This variant has been reported in 4 probands meeting phenotypic criteria, resulting in a total phenotype score of 2 (PS4_Moderate, Ambry Genetics, GeneDX internal data). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The results from more than 2 in silico splicing predictors indicate that this variant may affect splicing by disrupting the donor splice site of intron 13 of APC (PP3). This is confirmed by RT-PCR which demonstrate that the variant impacts splicing by leading to an in-frame exon skipping event in exon 13 r.1549_1626del78 (p.Ala517_Gln542del) (PS3_Moderate, Ambry internal data). 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_Moderate, PS4_Moderate, PP3, PM2_Supporting (VCEP specifications version 1; date of approval: 12/12/2022). LINK:https://erepo.genome.network/evrepo/ui/classification/CA16611623/MONDO:0021056/089

• Frequency: Genomes: not found (cov: 32)
• Consequence: APC NM_000038.6 splice_region, intron
• Scores: Splicing: ADA: 0.9996
• Clinical Significance: Likely pathogenic reviewed by expert panel P:3 U:2
• Conservation: PhyloP100: 6.73

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.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APC	NM_000038.6	c.1626+3A>G		splice_region_variant, intron_variant	Intron 13 of 15	ENST00000257430.9	NP_000029.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APC	ENST00000257430.9	c.1626+3A>G		splice_region_variant, intron_variant	Intron 13 of 15	5	NM_000038.6	ENSP00000257430.4
ENSG00000258864	ENST00000520401.1	n.111+3A>G		splice_region_variant, intron_variant	Intron 2 of 7	3		ENSP00000454861.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3 Uncertain:2

Revision: reviewed by expert panel

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:2

Feb 19, 2023

ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.1626+3A>G variant in APC is an intronic variant which is located at the 3rd nucleotide in intron 13. This variant has been reported in 4 probands meeting phenotypic criteria, resulting in a total phenotype score of 2 (PS4_Moderate, Ambry Genetics, GeneDX internal data). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The results from more than or equal to 2 in silico splicing predictors indicate that this variant may affect splicing by disrupting the donor splice site of intron 13 of APC (PP3). This is confirmed by RT-PCR which demonstrate that the variant impacts splicing by leading to an in-frame exon skipping event in exon 13 r.1549_1626del78 (p.Ala517_Gln542del) (PS3_Moderate, Ambry internal data). 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_Moderate, PS4_Moderate, PP3, PM2_Supporting (VCEP specifications version 1; date of approval: 12/12/2022). -

Jul 13, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 13 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 likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with clinical features of familial adenomatous polyposis (Invitae). ClinVar contains an entry for this variant (Variation ID: 411555). 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 skipping of exon 13, but is expected to preserve the integrity of the reading-frame (Invitae). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

Oct 01, 2021

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1626+3A>G intronic pathogenic variant results from an A to G substitution 3 nucleotides after coding exon 12 in the APC gene. This nucleotide position is highly conserved in available vertebrate species. This alteration has been observed in multiple individuals with a personal and/or family history that is consistent with APC-related disease (Ambry internal data). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). In silico splice site analysis for this alteration is inconclusive. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Nov 18, 2022

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes an A to G nucleotide substitution at the +3 position of intron 13 of the APC gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. To our knowledge, functional studies have not been reported for this variant nor has this variant been reported in individuals affected with hereditary cancer in the literature. This variant has been observed in individuals showing features of familial adenomatous polyposis (communication with an external laboratory). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion for a pathogenic role, the available evidence is insufficient to determine the role of this variant in disease conclusively due to the lack of understanding of the variant impact on RNA splicing. Therefore, this variant is classified as a Variant of Uncertain Significance. -

not specified Uncertain:1

Apr 26, 2019

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The APC c.1626+3A>G variant (rs1060503372) has not been reported in the medical literature, but is listed as a variant of uncertain clinical significance in ClinVar (Variation ID: 411555). It is absent from general population databases (Exome Variant Server and Genome Aggregation Database), indicating it is not a common polymorphism. This variant is located at a highly conserved nucleotide adjacent to the splice consensus sequence, and computational algorithms (Alamut v.2.11) predict that it affects the nearby canonical splice donor. However, due to the limited information regarding this variant, its clinical significance cannot be determined with certainty. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Uncertain	25
DANN	Uncertain	0.97

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.97
SpliceAI score (max)		0.13		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1060503372; hg19: chr5-112163706;