Is CD47 p.Val238Ile (c.712G>A) pathogenic?

CD47 p.Val238Ile (c.712G>A) is classified Uncertain significance in CD47 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-13). AlphaMissense: likely benign (0.1343); Very rare (popmax 0.00674%, afr).

How common is CD47 p.Val238Ile (c.712G>A) in the general population?

CD47 p.Val238Ile (c.712G>A) is very rare (popmax 0.00674%, afr) (gnomAD).

What do computational predictors say about CD47 p.Val238Ile (c.712G>A)?

AlphaMissense predicts likely benign (score 0.1343) — an in-silico prediction, not a clinical call.

CD47 p.Val238Ile

c.712G>A · rs1218151856 · VCV3140601

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1343 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00674%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1343	likely benign
REVEL	0.077	moderately benign-leaning
SaProt	LLR -5.07	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.33 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.9	GERP -2.8, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 12 kb · p 0.71 · regional, not allelic
Overall
CADD	19.91	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 0.00674% African / African-American · 5/74,220 alleles

Filtering AF 0.00257% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00163%

Overall 0.00237% 37/1,564,410 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00674%	14,844
Admixed American	0.00383%	26,141
European (non-Finnish)	0.00243%	41,163
Remaining individualsnot grpmax-eligible	0.00165%	60,636
South Asian	0.00118%	85,002

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: CD47
Protein: p.Val238Ile
Coding: c.712G>A
MANE Select: NM_001777
dbSNP: rs1218151856
Type: single nucleotide variant
Location: chr3:108058409 (GRCh38)
Gene constraint: LOEUF 0.725 · pLI 0.76 (gnomAD)
Structure: AlphaFold pLDDT 86.48 · 15 PDB
Residue 238: a disulfide bond; an α-helix

Full CD47 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD47 p.Ala178Gly Uncertain significance ★ ⚠ same type
CD47 p.Ala281Thr Uncertain significance ★ ⚠ same type
CD47 p.Asp104Asn Uncertain significance ★ ⚠ same type
CD47 p.Glu128Lys Uncertain significance ★ ⚠ same type
CD47 p.Gly318Ala Uncertain significance ★ ⚠ same type
CD47 p.Ile127Leu Uncertain significance ★ ⚠ same type
CD47 p.Ile150Val Uncertain significance ★ ⚠ same type
CD47 p.Ile153Val 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/cd47-p-val238ile (accessed [today's date]).

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