APOB p.Asp2162=
c.6486T>C · rs767577474 · VCV1539834
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.59e-05%, nfe)
Conditions
2
familial hypobetalipoproteinemia 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP 0.58, phastCons 1 |
| Overall | ||
| CADD | 5.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.59e-05%
European (non-Finnish) · 1/1,163,902 alleles
Overall
6.31e-05%
1/1,584,942 alleles · very rare
exomes 1/1,432,618 · genomes 0/152,324 · joint denominator
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
- APOB
- Protein
- p.Asp2162=
- Coding
- c.6486T>C
- MANE Select
- NM_000384
- dbSNP
- rs767577474
- Type
- single nucleotide variant
- Location
- chr2:21010382 (GRCh38)
- Gene constraint
- LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Residue 2162
- the 'heparin-binding' region
Similar variants
- APOB p.Asp2162Asn Benign/Likely benign ★★ same residue
- APOB p.Asp2162Tyr Uncertain significance ★ ⚠ same residue
- APOB c.1830-1G>A Pathogenic ★★ same condition
- APOB c.2604+1G>A Likely pathogenic ★★ same condition
- APOB c.537+1G>T Pathogenic/Likely pathogenic ★★ same condition
- APOB p.Arg1333Ter Pathogenic ★★ same condition
- APOB p.Arg2012Ter Pathogenic ★★ same condition
- APOB p.Arg2085Ter Pathogenic/Likely pathogenic ★★ same condition
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/apob-p-asp2162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown