Is CHST7 p.Val97Met (c.289G>A) pathogenic?

CHST7 p.Val97Met (c.289G>A) is classified Uncertain significance in CHST7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-04). AlphaMissense: likely benign (0.1236); Ultra-rare (popmax 0.0122%, afr).

How common is CHST7 p.Val97Met (c.289G>A) in the general population?

CHST7 p.Val97Met (c.289G>A) is ultra-rare (popmax 0.0122%, afr) (gnomAD).

What do computational predictors say about CHST7 p.Val97Met (c.289G>A)?

AlphaMissense predicts likely benign (score 0.1236) — an in-silico prediction, not a clinical call.

CHST7 p.Val97Met

c.289G>A · VCV4002794

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1236 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0122%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1236	likely benign
REVEL	0.107	moderately benign-leaning
SaProt	LLR -9.10	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 0.13	GERP -0.35
Regional constraint	o/e 0.73	unconstrained · MANE · 1,017 bp · p 1.6e-06 · regional, not allelic
Overall
CADD	11.32	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 0.0122% African / African-American · 7/57,427 alleles

Filtering AF 0.00565% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00404%

Overall 0.000579% 7/1,208,033 alleles · ultra-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: CHST7
Protein: p.Val97Met
Coding: c.289G>A
MANE Select: NM_019886
Type: single nucleotide variant
Location: chrX:46574220 (GRCh38)
Structure: AlphaFold pLDDT 80.60

Full CHST7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHST7 p.Asp266= Benign ★★ same type
CHST7 p.Ala172Thr Uncertain significance ★ ⚠ same type
CHST7 p.Ala337Thr Uncertain significance ★ ⚠ same type
CHST7 p.Ala413Ser Uncertain significance ★ ⚠ same type
CHST7 p.Ala413Thr Uncertain significance ★ ⚠ same type
CHST7 p.Ala453Val Uncertain significance ★ ⚠ same type
CHST7 p.Arg323Cys Uncertain significance ★ ⚠ same type
CHST7 p.Arg354Ser 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/chst7-p-val97met (accessed [today's date]).

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