TSPYL6 p.Asp149=
c.447C>T · rs61742696 · VCV773481
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.81%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -3.8 |
| Overall | ||
| CADD | 0.563 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.81%
African / African-American · 2,106/74,988 alleles
Filtering AF
2.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.67%
Overall
0.148%
2,389/1,613,818 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.81% | 36 |
| Remaining individualsnot grpmax-eligible | 0.219% | 456 |
| Admixed American | 0.152% | 659 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.00988% | 10,120 |
| European (non-Finnish) | 0.00347% | 28,781 |
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
- TSPYL6
- Protein
- p.Asp149=
- Coding
- c.447C>T
- MANE Select
- NM_138448 · reported on NM_001003937
- dbSNP
- rs61742696
- Type
- single nucleotide variant
- Location
- chr2:54255705 (GRCh38)
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/tspyl6-p-asp149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown