Is TNC p.Asp1098Val (c.3293A>T) pathogenic?

TNC p.Asp1098Val (c.3293A>T) is classified Uncertain significance in TNC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-23). AlphaMissense: likely benign (0.2643); Absent from gnomAD v4.1.

How common is TNC p.Asp1098Val (c.3293A>T) in the general population?

TNC p.Asp1098Val (c.3293A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TNC p.Asp1098Val (c.3293A>T)?

AlphaMissense predicts likely benign (score 0.2643) — an in-silico prediction, not a clinical call.

TNC p.Asp1098Val

c.3293A>T · VCV3327442

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2643 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.2643	likely benign
REVEL	0.36	indeterminate
SaProt	LLR -11.41	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.2	GERP 2.9, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 61 kb · p 0.8 · regional, not allelic
Overall
CADD	23.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TNC
Protein: p.Asp1098Val
Coding: c.3293A>T
MANE Select: NM_002160
Type: single nucleotide variant
Location: chr9:115064841 (GRCh38)
Gene constraint: LOEUF 0.608 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.48 · 21 PDB
Residue 1098: the fibronectin type-iii 6 domain

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

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TNC p.Asp2059Glu Uncertain significance ★★ ⚠ same type
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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-asp1098val (accessed [today's date]).

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