TANC2 p.Val63=
c.189C>T · rs370460475 · VCV3250630
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.229%, sas)
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 0.37 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 3.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.229%
South Asian · 206/90,046 alleles
Filtering AF
0.203%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.193%
Overall
0.0199%
321/1,609,720 alleles · rare
exomes 301/1,457,406 · genomes 20/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.229% | 437 |
| Middle Eastern | 0.0662% | 1,512 |
| Finnishnot grpmax-eligible | 0.022% | 4,551 |
| Remaining individualsnot grpmax-eligible | 0.0177% | 5,663 |
| European (non-Finnish) | 0.00688% | 14,542 |
| Admixed American | 0.00336% | 29,770 |
| African / African-American | 0.00267% | 37,492 |
| East Asian | 0.00223% | 44,760 |
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
- TANC2
- Protein
- p.Val63=
- Coding
- c.189C>T
- MANE Select
- NM_001394998
- dbSNP
- rs370460475
- Type
- single nucleotide variant
- Location
- chr17:63099224 (GRCh38)
- Gene constraint
- LOEUF 0.17 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.92
- Residue 63
- the 'disordered' region
Similar variants
- TANC2 p.Arg1516Gln Uncertain significance ★★ ⚠ same type
- TANC2 p.Arg1741Gln Uncertain significance ★★ ⚠ same type
- TANC2 p.Arg1923Ter Uncertain significance ★★ same type
- TANC2 p.Arg268Cys Uncertain significance ★★ ⚠ same type
- TANC2 p.Arg388His Uncertain significance ★★ ⚠ same type
- TANC2 p.Arg466Lys Uncertain significance ★★ ⚠ same type
- TANC2 p.Arg563Trp Uncertain significance ★★ ⚠ same type
- TANC2 p.Arg834Cys 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/tanc2-p-val63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown