Is CHST9 p.Val203= (c.609A>G) pathogenic?

CHST9 p.Val203= (c.609A>G) is classified Likely benign in CHST9 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-01). Low-frequency (popmax 1.01%, sas).

How common is CHST9 p.Val203= (c.609A>G) in the general population?

CHST9 p.Val203= (c.609A>G) is low-frequency (popmax 1.01%, sas) (gnomAD).

CHST9 p.Val203=

c.609A>G · rs138794390 · VCV2648627

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.01%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.77	GERP -5.3, phastCons 0.009
Overall
CADD	0.739	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.01% South Asian · 918/91,068 alleles

Filtering AF 0.954% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.932%

Overall 0.312% 5,039/1,613,922 alleles · low-frequency

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.75%	57
South Asiangrpmax	1.01%	99
Middle Eastern	0.561%	178
Finnishnot grpmax-eligible	0.523%	191
Remaining individualsnot grpmax-eligible	0.434%	231
Admixed American	0.298%	335
European (non-Finnish)	0.234%	427
African / African-American	0.0293%	3,410
East Asian	0.00446%	22,436

Ashkenazi Jewish 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: CHST9
Protein: p.Val203=
Coding: c.609A>G
dbSNP: rs138794390
Type: single nucleotide variant
Location: chr18:26916982 (GRCh38)

Full CHST9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/chst9-p-val203 (accessed [today's date]).

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