NFASC p.Pro939=
c.2817G>A · rs141864015 · VCV3025406
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.273%, 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 -6.1 | GERP -5.3 |
| Overall | ||
| CADD | 3.168 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.273%
African / African-American · 205/75,046 alleles
Filtering AF
0.243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.231%
Overall
0.0188%
303/1,613,130 alleles · rare
exomes 179/1,460,788 · genomes 124/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.273% | 366 |
| Admixed American | 0.0633% | 1,580 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,679 |
| European (non-Finnish) | 0.00382% | 26,201 |
| South Asian | 0.00329% | 30,350 |
| East Asian | 0.00223% | 44,878 |
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
- NFASC
- Protein
- p.Pro939=
- Coding
- c.2817G>A
- MANE Select
- NM_001005388 · reported on NM_001160331
- dbSNP
- rs141864015
- Type
- single nucleotide variant
- Location
- chr1:204986107 (GRCh38)
- Gene constraint
- LOEUF 0.362 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.23 · 2 PDB
- Residue 939
- the fibronectin type-iii 4 domain; a UniProt-annotated variant site (in nedcpmd; uncertain significance; no protein expression)
Similar variants
- NFASC p.Ala939Thr Uncertain significance ★ same residue
- NFASC p.Pro939fs Pathogenic same residue
- NFASC c.2593+5G>A Uncertain significance ★★ same type
- NFASC p.Ala253Thr Uncertain significance ★★ same type
- NFASC p.Arg133His Uncertain significance ★★ same type
- NFASC p.Arg436Gln Uncertain significance ★★ same type
- NFASC p.Asn655Asp Uncertain significance ★★ same type
- NFASC p.Asp1038Ala 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/nfasc-p-pro939 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown