Is CD7 p.Asn237Ser (c.710A>G) pathogenic?

CD7 p.Asn237Ser (c.710A>G) is classified Uncertain significance in CD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-29). AlphaMissense: likely benign (0.1301); Very rare (popmax 0.007%, nfe).

How common is CD7 p.Asn237Ser (c.710A>G) in the general population?

CD7 p.Asn237Ser (c.710A>G) is very rare (popmax 0.007%, nfe) (gnomAD).

What do computational predictors say about CD7 p.Asn237Ser (c.710A>G)?

AlphaMissense predicts likely benign (score 0.1301) — an in-silico prediction, not a clinical call.

CD7 p.Asn237Ser

c.710A>G · VCV4650693

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1301 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.007%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1301	likely benign
REVEL	0.059	moderately benign-leaning
SaProt	LLR -5.20	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 0.063	GERP -1.3, phastCons 0.001
Regional constraint	o/e 0.89	unconstrained · MANE · 2,171 bp · p 0.046 · regional, not allelic
Overall
CADD	14.34	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 0.007% European (non-Finnish) · 82/1,171,094 alleles

Filtering AF 0.00575% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00529%

Overall 0.00518% 83/1,602,884 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.007%	14,282
Remaining individualsnot grpmax-eligible	0.00161%	62,084

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.Asn237Ser
Coding: c.710A>G
MANE Select: NM_006137
Type: single nucleotide variant
Location: chr17:82315334 (GRCh38)
Gene constraint: LOEUF 1.673 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.51 · 2 PDB

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-asn237ser (accessed [today's date]).

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