NARS2 p.Ser103=
c.309C>G · rs375477311 · VCV709887
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, 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 2.2 | GERP 0.6, phastCons 1 |
| Overall | ||
| CADD | 7.713 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,862 alleles
Filtering AF
0.00172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00149%
Overall
0.00198%
32/1,612,598 alleles · very rare
exomes 29/1,460,518 · genomes 3/152,080 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,954 |
| European (non-Finnish) | 0.00246% | 40,661 |
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
- NARS2
- Protein
- p.Ser103=
- Coding
- c.309C>G
- MANE Select
- NM_024678
- dbSNP
- rs375477311
- Type
- single nucleotide variant
- Location
- chr11:78568695 (GRCh38)
- Gene constraint
- LOEUF 1.253 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.59
Similar variants
- NARS2 p.Arg140Ter Pathogenic ★★ same type
- NARS2 p.Arg243Ter Pathogenic/Likely pathogenic ★★ same type
- NARS2 p.Asn317= Pathogenic/Likely pathogenic ★★ same type
- NARS2 p.Tyr323Ter Pathogenic/Likely pathogenic ★★ same type
- NARS2 p.Tyr412Ter Pathogenic ★★ same type
- NARS2 c.689+6A>G Uncertain significance ★★ same type
- NARS2 p.Ala17Val Uncertain significance ★★ ⚠ same type
- NARS2 p.Arg140Pro 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/nars2-p-ser103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown