TNC p.Gln603=
c.1809A>G · rs3827815 · VCV1277030
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 16.9%, mid) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.59 | phastCons 1 |
| Overall | ||
| CADD | 2.885 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
16.9%
Middle Eastern · 1,023/6,062 alleles
Filtering AF
16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 15.7%
Overall
10.2%
163,896/1,613,148 alleles · common
exomes 149,885/1,460,928 · genomes 14,011/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 16.9% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 13.3% | 7 |
| East Asian | 11.4% | 9 |
| South Asian | 11% | 9 |
| Remaining individualsnot grpmax-eligible | 10.4% | 10 |
| European (non-Finnish) | 10.4% | 10 |
| Admixed American | 9.26% | 11 |
| Finnishnot grpmax-eligible | 8.24% | 12 |
| African / African-American | 5.18% | 19 |
| Amishnot grpmax-eligible | 4.07% | 25 |
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
- TNC
- Protein
- p.Gln603=
- Coding
- c.1809A>G
- MANE Select
- NM_002160
- dbSNP
- rs3827815
- Type
- single nucleotide variant
- Location
- chr9:115085922 (GRCh38)
- Gene constraint
- LOEUF 0.608 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.48 · 21 PDB
- Residue 603
- the egf-like 15 domain
Similar variants
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- TNC p.Arg608Cys Uncertain significance ★★ ⚠ same type
- TNC p.Arg669His Uncertain significance ★★ ⚠ same type
- TNC p.Arg747Trp Uncertain significance ★★ ⚠ same type
- TNC p.Asn507Lys Uncertain significance ★★ ⚠ same type
- TNC p.Asp2059Glu Uncertain significance ★★ ⚠ same type
- TNC p.Asp831Asn Uncertain significance ★★ ⚠ same type
- TNC p.Asp971Asn 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/tnc-p-gln603 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown