Is CD7 p.Arg83Trp (c.247C>T) pathogenic?

CD7 p.Arg83Trp (c.247C>T) is classified Uncertain significance in CD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). AlphaMissense: likely benign (0.2623); Very rare (popmax 0.00534%, afr).

How common is CD7 p.Arg83Trp (c.247C>T) in the general population?

CD7 p.Arg83Trp (c.247C>T) is very rare (popmax 0.00534%, afr) (gnomAD).

What do computational predictors say about CD7 p.Arg83Trp (c.247C>T)?

AlphaMissense predicts likely benign (score 0.2623) — an in-silico prediction, not a clinical call.

CD7 p.Arg83Trp

c.247C>T · VCV3998322

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2623 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00534%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2623	likely benign
REVEL	0.143	moderately benign-leaning
SaProt	LLR -11.74	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.4	GERP -3.2
Regional constraint	o/e 0.89	unconstrained · MANE · 2,171 bp · p 0.046 · regional, not allelic
Overall
CADD	14.6	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00534% African / African-American · 4/74,922 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.00155% 25/1,613,840 alleles · very rare exomes 24/1,461,652 · genomes 1/152,188 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0064%	15,620
African / African-Americangrpmax	0.00534%	18,730
Admixed American	0.005%	20,000
East Asian	0.00223%	44,906
South Asian	0.0011%	91,088
European (non-Finnish)	0.00102%	98,331

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CD7
Protein: p.Arg83Trp
Coding: c.247C>T
MANE Select: NM_006137
Type: single nucleotide variant
Location: chr17:82316817 (GRCh38)
Gene constraint: LOEUF 1.673 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.51 · 2 PDB
Residue 83: the ig-like domain

Full CD7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD7 p.Ala145Thr Uncertain significance ★ ⚠ same type
CD7 p.Ala154Asp Uncertain significance ★ ⚠ same type
CD7 p.Ala154Thr Uncertain significance ★ ⚠ same type
CD7 p.Ala15Val Uncertain significance ★ ⚠ same type
CD7 p.Ala17Ser Uncertain significance ★ ⚠ same type
CD7 p.Ala184Val Uncertain significance ★ ⚠ same type
CD7 p.Ala217Thr Uncertain significance ★ ⚠ same type
CD7 p.Ala218Thr 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/cd7-p-arg83trp (accessed [today's date]).

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