Is APC p.Arg2670= (c.8010A>G) pathogenic?

APC p.Arg2670= (c.8010A>G) is classified Benign/Likely benign in APC (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-05-22). Very rare (popmax 0.00167%, amr); Associated with classic or attenuated familial adenomatous polyposis.

What condition is associated with APC p.Arg2670= (c.8010A>G)?

APC p.Arg2670= (c.8010A>G) is associated with classic or attenuated familial adenomatous polyposis, hereditary neoplastic syndrome, familial adenomatous polyposis 1 (ClinVar).

How common is APC p.Arg2670= (c.8010A>G) in the general population?

APC p.Arg2670= (c.8010A>G) is very rare (popmax 0.00167%, amr) (gnomAD).

APC p.Arg2670=

c.8010A>G · rs786201524 · VCV184540

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

classic or attenuated familial adenomatous polyposis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.58	GERP -5.9, phastCons 0.89
Overall
CADD	2.471	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,976 alleles

Filtering AF 0.000429% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000312%

Overall 0.000682% 11/1,613,876 alleles · very rare exomes 7/1,461,758 · genomes 4/152,118 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,976
European (non-Finnish)	0.000848%	117,993

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: APC
Protein: p.Arg2670=
Coding: c.8010A>G
MANE Select: NM_000038
dbSNP: rs786201524
Type: single nucleotide variant
Location: chr5:112843604 (GRCh38)
Gene constraint: LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2670: the 'basic region' region; the 'interaction with dlg1' region; the 'disordered' region

Full APC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

classic or attenuated familial adenomatous polyposis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome familial adenomatous polyposis 1

Similar variants

APC p.Arg2670Gly Uncertain significance ★★ ⚠ same residue
APC p.Arg2670Ile Uncertain significance ★★ same residue
APC p.Arg2670Lys Uncertain significance ★★ same residue
APC p.Arg2670Thr Uncertain significance ★ same residue
APC c.1312+3A>C Likely pathogenic ★★★ same condition
APC c.1312+3A>G Pathogenic ★★★ same condition
APC c.1312+5G>A Likely pathogenic ★★★ same condition
APC c.1312+5G>C Likely pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/apc-p-arg2670 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown