TYMS p.Gln32=
c.96G>A · rs1446885716 · VCV762218
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00106%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.4 | GERP 0.58, phastCons 1 |
| Overall | ||
| CADD | 11.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00106%
European (non-Finnish) · 12/1,130,494 alleles
Filtering AF
0.000566%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000447%
Overall
0.000805%
12/1,491,398 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
- TYMS
- Protein
- p.Gln32=
- Coding
- c.96G>A
- MANE Select
- NM_001071
- dbSNP
- rs1446885716
- Type
- single nucleotide variant
- Location
- chr18:657838 (GRCh38)
- Gene constraint
- LOEUF 0.882 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.05 · 61 PDB
- Residue 32
- an α-helix
Similar variants
- TYMS p.Arg115Ter Pathogenic ★ same type
- TYMS p.Ala4Ser Uncertain significance ★ ⚠ same type
- TYMS p.Asp148Glu Uncertain significance ★ ⚠ same type
- TYMS p.Glu87Lys Uncertain significance ★ ⚠ same type
- TYMS p.Gly29Arg Uncertain significance ★ ⚠ same type
- TYMS p.Pro15Arg Uncertain significance ★ ⚠ same type
- TYMS p.Pro15His Uncertain significance ★ ⚠ same type
- TYMS p.Pro24Thr 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/tyms-p-gln32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown