rs878853426

Variant names:

• chr5-112837905-GA-G
• rs878853426
• NM_000038.6:c.2314delA

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.2314delA​(p.Thr772LeufsTer5) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: APC NM_000038.6 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• 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: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 270 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 5-112837905-GA-G is Pathogenic according to our data. Variant chr5-112837905-GA-G is described in ClinVar as [Pathogenic]. Clinvar id is 236573.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112837905-GA-G is described in Lovd as [Pathogenic]. Variant chr5-112837905-GA-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APC	NM_000038.6	c.2314delA	p.Thr772LeufsTer5	frameshift_variant	Exon 16 of 16	ENST00000257430.9	NP_000029.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APC	ENST00000257430.9	c.2314delA	p.Thr772LeufsTer5	frameshift_variant	Exon 16 of 16	5	NM_000038.6	ENSP00000257430.4
ENSG00000258864	ENST00000520401.1	n.228+8936delA		intron_variant	Intron 3 of 7	3		ENSP00000454861.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:3

Jan 02, 2016

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. Truncating variants in APC are known to be pathogenic. This particular truncation has been reported in the literature  in an individual with familial adenomatous polyposis (PMID: 10083733). This variant is located in the last coding exon of APC. However, other downstream, pathogenic truncating variants have been reported in exon 16 (PMID: 20223039, 11247896, 1316610) This sequence change deletes 1 nucleotide from exon 16 of the APC mRNA (c.2314delA), causing a frameshift at codon 772. This creates a premature translational stop signal in the last exon of the APC mRNA (p.Thr772Leufs*5). While this is not anticipated to result in nonsense mediated decay, it is expected to result in a truncated APC protein. -

May 04, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -

Jan 02, 2016

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change deletes 1 nucleotide from exon 16 of the APC mRNA (c.2314delA), causing a frameshift at codon 772. This creates a premature translational stop signal in the last exon of the APC mRNA (p.Thr772Leufs*5). While this is not anticipated to result in nonsense mediated decay, it is expected to result in a truncated APC protein. Truncating variants in APC are known to be pathogenic. This particular truncation has been reported in the literature in an individual with familial adenomatous polyposis (PMID: 10083733). This variant is located in the last coding exon of APC. However, other downstream, pathogenic truncating variants have been reported in exon 16 (PMID: 20223039, 11247896, 1316610) For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs878853426; hg19: chr5-112173602;