NTRK2 p.Ser2=
c.6G>T · rs199851011 · VCV1575375
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 6.6 | GERP -0.059, phastCons 1 |
| Overall | ||
| CADD | 13.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,026 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000682%
11/1,612,888 alleles · very rare
exomes 11/1,460,550 · genomes 0/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,026 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,436 |
| European (non-Finnish) | 0.000763% | 131,115 |
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
- NTRK2
- Protein
- p.Ser2=
- Coding
- c.6G>T
- MANE Select
- NM_006180
- dbSNP
- rs199851011
- Type
- single nucleotide variant
- Location
- chr9:84670754 (GRCh38)
- Gene constraint
- LOEUF 0.123 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.53 · 9 PDB
Similar variants
- NTRK2 p.Ser2Leu Uncertain significance ★ ⚠ same residue
- NTRK2 p.Ser2Trp Uncertain significance ★ ⚠ same residue
- NTRK2 p.Arg551Gln Likely pathogenic ★★ same type
- NTRK2 p.Tyr434Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- NTRK2 p.Ala440Val Uncertain significance ★★ ⚠ same type
- NTRK2 p.Arg124Gly Uncertain significance ★★ ⚠ same type
- NTRK2 p.Arg478Lys Uncertain significance ★★ same type
- NTRK2 p.Arg57Ile 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/ntrk2-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown