Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.38%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.57 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.64 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 8.5 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 18.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.38%
African / African-American · 5,531/74,996 alleles
Filtering AF
7.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.15%
Overall
0.41%
6,623/1,613,840 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.38% | 14 |
| Middle Eastern | 0.777% | 129 |
| Remaining individualsnot grpmax-eligible | 0.55% | 182 |
| Admixed American | 0.495% | 202 |
| Ashkenazi Jewishnot grpmax-eligible | 0.351% | 285 |
| European (non-Finnish) | 0.0238% | 4,199 |
| South Asian | 0.0165% | 6,071 |
| Finnishnot grpmax-eligible | 0.00627% | 15,957 |
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
- ABHD2
- Protein
- p.Val420=
- Coding
- c.1260G>A
- MANE Select
- NM_152924
- dbSNP
- rs8029350
- Type
- single nucleotide variant
- Location
- chr15:89195405 (GRCh38)
- Gene constraint
- LOEUF 0.57 · pLI 0.55 (gnomAD)
- Structure
- AlphaFold pLDDT 91.06
Similar variants
- ABHD2 p.Val420Met Uncertain significance ★ ⚠ same residue
- ABHD2 p.His312= Benign ★★ same type
- ABHD2 p.Tyr400= Benign ★★ same type
- ABHD2 p.Ala222Gly Uncertain significance ★ ⚠ same type
- ABHD2 p.Ala274Thr Uncertain significance ★ ⚠ same type
- ABHD2 p.Arg175Cys Uncertain significance ★ ⚠ same type
- ABHD2 p.Arg254Gln Uncertain significance ★ ⚠ same type
- ABHD2 p.Arg293Gln 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/abhd2-p-val420 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown