5-112844102-G-A

Variant names:

• chr5-112844102-G-A
• rs878853479
• NM_000038.6:c.8508G>A

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM2 BP4_Strong BP6_Very_Strong BP7

The NM_000038.6(APC):​c.8508G>A​(p.Gly2836Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G2836G) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: APC NM_000038.6 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.319
• Publications: 0 publications found

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]

APC Gene-Disease associations (from GenCC):

• classic or attenuated familial adenomatous polyposis

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• desmoid tumor

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Genomics England PanelApp
• familial adenomatous polyposis 1

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics
• gastric adenocarcinoma and proximal polyposis of the stomach

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
• sarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• APC-related attenuated familial adenomatous polyposis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Turcot syndrome with polyposis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Cenani-Lenz syndactyly syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000258864 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 5-112844102-G-A is Benign according to our data. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112844102-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 1332559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.319 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APC	NM_000038.6	c.8508G>A	p.Gly2836Gly	synonymous_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.8508G>A	p.Gly2836Gly	synonymous_variant	Exon 16 of 16	5	NM_000038.6	ENSP00000257430.4
ENSG00000258864	ENST00000520401.1	n.229-12547G>A		intron_variant	Intron 3 of 7	3		ENSP00000454861.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000801 AC: 2 AN: 249840 AF XY: 0.0000148

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000583

Gnomad ASJ exome AF: 0.00

Gnomad EAS 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: 0.00000205 AC: 3 AN: 1460466 Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3 AN XY: 726492

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000299 AC: 1 AN: 33412

American (AMR) AF: 0.0000450 AC: 2 AN: 44474

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26072

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00 AC: 0 AN: 85928

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53406

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5758

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111378

Other (OTH) AF: 0.00 AC: 0 AN: 60342

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial adenomatous polyposis 1 Benign:2

Apr 16, 2024

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. -

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:1

Mar 22, 2021

Color Diagnostics, LLC DBA Color Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	4.9
DANN	Benign	0.83
PhyloP100		0.32

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

Other links and lift over

dbSNP: rs878853479; hg19: chr5-112179799;