GPATCH4 c.348+115G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.18%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.039 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| Splice region | donor +115 | deep intronic (+115 nt into the intron) |
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.061 | GERP -2.5 |
| Non-coding constraint | Z 2.08 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 6.111 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.18%
Middle Eastern · 97/4,452 alleles
Filtering AF
1.83%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.7%
Overall
0.695%
5,357/770,508 alleles · low-frequency
exomes 4,506/618,266 · genomes 851/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.18% | 46 |
| South Asian | 0.958% | 104 |
| European (non-Finnish) | 0.832% | 120 |
| Remaining individualsnot grpmax-eligible | 0.752% | 133 |
| Ashkenazi Jewishnot grpmax-eligible | 0.602% | 166 |
| Admixed American | 0.511% | 196 |
| Finnishnot grpmax-eligible | 0.503% | 199 |
| African / African-American | 0.14% | 713 |
| East Asian | 0.00247% | 40,490 |
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
- GPATCH4
- Coding
- c.348+115G>A
- dbSNP
- rs111439860
- Type
- single nucleotide variant
- Location
- chr1:156597920 (GRCh38)
- Gene constraint
- LOEUF 1.669 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.52
Similar variants
- GPATCH4 c.-65A>C Uncertain significance ★ same type
- GPATCH4 c.-74G>C Uncertain significance ★ same type
- GPATCH4 c.-79G>C Uncertain significance ★ same type
- GPATCH4 p.Ala162Thr Uncertain significance ★ same type
- GPATCH4 p.Ala174Pro Uncertain significance ★ same type
- GPATCH4 p.Ala219Val Uncertain significance ★ same type
- GPATCH4 p.Ala316Val Uncertain significance ★ same type
- GPATCH4 p.Arg167His 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/gpatch4-c-348-plus-115g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown