ALPL c.792+207C>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 45.4%, eas) — 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 | ||
| Splice region | donor +207 | deep intronic (+207 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -1.7 |
| Non-coding constraint | Z 3.14 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 2.225 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
45.4%
East Asian · 2,317/5,102 alleles
Filtering AF
43.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 43.2%
Overall
17.6%
26,791/151,862 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 45.4% | 2 |
| South Asian | 23.2% | 4 |
| African / African-American | 23.1% | 4 |
| Admixed American | 21.6% | 5 |
| Finnishnot grpmax-eligible | 18.8% | 5 |
| Remaining individualsnot grpmax-eligible | 17.8% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 14% | 7 |
| Amishnot grpmax-eligible | 11.8% | 8 |
| Middle Eastern | 11.6% | 9 |
| European (non-Finnish) | 11.1% | 9 |
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
- ALPL
- Coding
- c.792+207C>T
- MANE Select
- NM_000478
- dbSNP
- rs3738096
- Type
- single nucleotide variant
- Location
- chr1:21568454 (GRCh38)
- Gene constraint
- LOEUF 0.987 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.74 · 5 PDB
Similar variants
- ALPL c.1190-2A>T Pathogenic ★★ same type
- ALPL c.182-1G>A Pathogenic/Likely pathogenic ★★ same type
- ALPL c.182-2A>G Pathogenic/Likely pathogenic ★★ same type
- ALPL c.297+1G>A Pathogenic/Likely pathogenic ★★ same type
- ALPL c.298-1G>A Pathogenic ★★ same type
- ALPL c.472+1G>A Pathogenic ★★ same type
- ALPL c.62-1G>C Pathogenic/Likely pathogenic ★★ same type
- ALPL c.648+1G>A Pathogenic ★★ 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/alpl-c-792-plus-207c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown