NHS p.Phe894=
c.2682C>T · rs773347582 · VCV2728949
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0218%, amr)
Conditions
1
Nance-Horan syndrome
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 0.86 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 6.448 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0218%
Admixed American · 10/45,804 alleles
Filtering AF
0.0118%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.009%
Overall
0.00231%
28/1,210,227 alleles · ultra-rare
exomes 14/1,098,124 · genomes 14/112,103 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0218% | 4,580 |
| African / African-American | 0.00873% | 11,454 |
| Remaining individualsnot grpmax-eligible | 0.0063% | 15,873 |
| East Asian | 0.00296% | 33,756 |
| South Asian | 0.00176% | 56,825 |
| European (non-Finnish) | 0.000894% | 111,913 |
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
- NHS
- Protein
- p.Phe894=
- Coding
- c.2682C>T
- MANE Select
- NM_001291867
- dbSNP
- rs773347582
- Type
- single nucleotide variant
- Location
- chrX:17726788 (GRCh38)
- Structure
- AlphaFold pLDDT 43.65
Similar variants
- NHS p.Arg248Ter Pathogenic ★★ same condition
- NHS p.Arg394Ter Pathogenic ★★ same condition
- NHS p.Arg900Ter Pathogenic ★★ same condition
- NHS p.Gln411Ter Pathogenic ★★ same condition
- NHS p.Gln80Ter Pathogenic/Likely pathogenic ★★ same condition
- NHS p.Ala564Val Uncertain significance ★★ same condition
- NHS p.Ala745Val Uncertain significance ★★ same condition
- NHS p.Arg162Cys Uncertain significance ★★ same condition
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/nhs-p-phe894 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown