Is CEACAM7 p.Val54Ile (c.160G>A) pathogenic?

CEACAM7 p.Val54Ile (c.160G>A) is classified Uncertain significance in CEACAM7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-03). AlphaMissense: likely benign (0.0878); Ultra-rare (popmax 0.0156%, eas).

How common is CEACAM7 p.Val54Ile (c.160G>A) in the general population?

CEACAM7 p.Val54Ile (c.160G>A) is ultra-rare (popmax 0.0156%, eas) (gnomAD).

What do computational predictors say about CEACAM7 p.Val54Ile (c.160G>A)?

AlphaMissense predicts likely benign (score 0.0878) — an in-silico prediction, not a clinical call.

CEACAM7 p.Val54Ile

c.160G>A · VCV3489886

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0878 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0156%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0878	likely benign
REVEL	0.08	moderately benign-leaning
SaProt	LLR -7.21	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -8	GERP -3.5
Regional constraint	o/e 0.98	unconstrained · MANE · 11 kb · p 0.74 · regional, not allelic
Overall
CADD	5.889	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0156% East Asian · 7/44,886 alleles

Filtering AF 0.00726% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00514%

Overall 0.000682% 11/1,614,064 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0156%	6,412
Remaining individualsnot grpmax-eligible	0.0048%	20,837
South Asian	0.0011%	91,068

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: CEACAM7
Protein: p.Val54Ile
Coding: c.160G>A
MANE Select: NM_001291485
Type: single nucleotide variant
Location: chr19:41687126 (GRCh38)
Gene constraint: LOEUF 1.373 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.92 · 1 PDB
Residue 54: a β-strand; the ig-like v-type domain

Full CEACAM7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEACAM7 p.Ala251Thr Uncertain significance ★ ⚠ same type
CEACAM7 p.Ala46Ser Uncertain significance ★ ⚠ same type
CEACAM7 p.Ala46Thr Uncertain significance ★ ⚠ same type
CEACAM7 p.Ala6Thr Uncertain significance ★ ⚠ same type
CEACAM7 p.Arg226Cys Uncertain significance ★ ⚠ same type
CEACAM7 p.Arg235His Uncertain significance ★ ⚠ same type
CEACAM7 p.Arg99Gln Uncertain significance ★ ⚠ same type
CEACAM7 p.Asn156Ser Uncertain significance ★ ⚠ same type

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/ceacam7-p-val54ile (accessed [today's date]).

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