Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.45%, afr) — too common for a highly-penetrant pathogenic allele
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 0.32 | GERP -5.8, phastCons 0.98 |
| Overall | ||
| CADD | 5.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.45%
African / African-American · 6,333/74,980 alleles
Filtering AF
8.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.2%
Overall
0.452%
7,296/1,612,916 alleles · common
exomes 3,669/1,460,758 · genomes 3,627/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.45% | 12 |
| Admixed American | 0.57% | 175 |
| Remaining individualsnot grpmax-eligible | 0.565% | 177 |
| Middle Eastern | 0.413% | 242 |
| South Asian | 0.0593% | 1,687 |
| European (non-Finnish) | 0.0158% | 6,310 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,596 |
| East Asian | 0.00223% | 44,830 |
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
- JPH3
- Protein
- p.Val344=
- Coding
- c.1032C>T
- MANE Select
- NM_020655
- dbSNP
- rs8051490
- Type
- single nucleotide variant
- Location
- chr16:87644907 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
Similar variants
- JPH3 p.Val344Ile Uncertain significance ★ ⚠ same residue
- JPH3 p.Arg319Trp Uncertain significance ★★ ⚠ same type
- JPH3 p.Leu266Val Uncertain significance ★★ ⚠ same type
- JPH3 p.Thr175Met Uncertain significance ★★ ⚠ same type
- JPH3 c.2167-9C>G Benign/Likely benign ★★ same type
- JPH3 p.Ala271= Benign/Likely benign ★★ same type
- JPH3 p.Ala366= Likely benign ★★ same type
- JPH3 p.Ala384= Likely benign ★★ 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/jph3-p-val344 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown