NHS p.Arg397=
c.1191G>A · rs767900191 · VCV3068838
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00873%, 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 2.6 | GERP 0.12, phastCons 1 |
| Overall | ||
| CADD | 8.711 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00873%
African / African-American · 5/57,270 alleles
Filtering AF
0.00338%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00215%
Overall
0.000413%
5/1,210,386 alleles · very rare
exomes 2/1,098,078 · genomes 3/112,308 · joint denominator
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.Arg397=
- Coding
- c.1191G>A
- MANE Select
- NM_001291867
- dbSNP
- rs767900191
- Type
- single nucleotide variant
- Location
- chrX:17724381 (GRCh38)
- Structure
- AlphaFold pLDDT 43.65
Similar variants
- NHS p.Arg248Ter Pathogenic ★★ same type
- NHS p.Arg394Ter Pathogenic ★★ same type
- NHS p.Arg900Ter Pathogenic ★★ same type
- NHS p.Gln411Ter Pathogenic ★★ same type
- NHS p.Gln80Ter Pathogenic/Likely pathogenic ★★ same type
- NHS p.Ala564Val Uncertain significance ★★ same type
- NHS p.Ala745Val Uncertain significance ★★ same type
- NHS p.Arg162Cys 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/nhs-p-arg397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown