Is CD47 p.Trp2Ter (c.5G>A) pathogenic?

CD47 p.Trp2Ter (c.5G>A) is classified Uncertain significance in CD47 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). Very rare (popmax 0.000446%, nfe).

How common is CD47 p.Trp2Ter (c.5G>A) in the general population?

CD47 p.Trp2Ter (c.5G>A) is very rare (popmax 0.000446%, nfe) (gnomAD).

CD47 p.Trp2Ter

c.5G>A · VCV4279818

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000446%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 11
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.6	GERP 0.87, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000446% European (non-Finnish) · 5/1,120,220 alleles

Filtering AF 0.000131% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.5e-05%

Overall 0.000377% 5/1,327,614 alleles · very rare

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.Trp2Ter
Coding: c.5G>A
MANE Select: NM_001777
Type: single nucleotide variant
Location: chr3:108090904 (GRCh38)
Gene constraint: LOEUF 0.725 · pLI 0.76 (gnomAD)
Structure: AlphaFold pLDDT 86.48 · 15 PDB

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-trp2ter (accessed [today's date]).

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