TERF2IP p.Pro103=
c.309C>A · rs1005356967 · VCV1727554
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00949%, afr)
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 -0.11 | GERP -3.4 |
| Overall | ||
| CADD | 3.186 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00949%
African / African-American · 7/73,770 alleles
Filtering AF
0.00443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00313%
Overall
0.000515%
8/1,551,900 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00949% | 10,539 |
| European (non-Finnish) | 8.69e-05% | 1,150,674 |
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.Pro103=
- Coding
- c.309C>A
- MANE Select
- NM_018975
- dbSNP
- rs1005356967
- Type
- single nucleotide variant
- Location
- chr16:75648191 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.76 · 5 PDB
Similar variants
- TERF2IP p.Pro103Leu Uncertain significance ★★ ⚠ same residue
- TERF2IP p.Pro103Thr Uncertain significance ★★ ⚠ same residue
- TERF2IP p.Pro103Ala Uncertain significance ★ ⚠ same residue
- TERF2IP p.Pro103Ser Conflicting classifications of pathogenicity ★ ⚠ 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
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-pro103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown