TERF2IP p.Ile79=
c.237C>T · rs960215333 · VCV1790413
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0185%, mid)
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 0.73 | GERP -0.14, phastCons 1 |
| Overall | ||
| CADD | 12.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0185%
Middle Eastern · 1/5,418 alleles
Filtering AF
0.00533%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00384%
Overall
0.00173%
27/1,558,764 alleles · ultra-rare
exomes 25/1,406,488 · genomes 2/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0185% | 5,418 |
| African / African-American | 0.0108% | 9,264 |
| Remaining individualsnot grpmax-eligible | 0.00498% | 20,061 |
| European (non-Finnish) | 0.0013% | 76,844 |
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
- TERF2IP
- Protein
- p.Ile79=
- Coding
- c.237C>T
- MANE Select
- NM_018975
- dbSNP
- rs960215333
- Type
- single nucleotide variant
- Location
- chr16:75648119 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.76 · 5 PDB
- Residue 79
- the brct domain
Similar variants
- TERF2IP p.Ile79Asn Uncertain significance ★★ ⚠ same residue
- TERF2IP p.Ala123Gly Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala200Gly Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala387Val Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala61Thr Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala65Thr Uncertain significance ★★ ⚠ same type
- TERF2IP p.Arg133Gln Uncertain significance ★★ ⚠ same type
- TERF2IP p.Arg378Ser 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/terf2ip-p-ile79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown