APOB p.Phe3010=
c.9030T>C · rs775869949 · VCV1765541
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
Cardiovascular phenotype
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 -0.29 | GERP -3.4 |
| Overall | ||
| CADD | 0.173 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,958 alleles
Overall
6.2e-05%
1/1,614,100 alleles · very rare
exomes 1/1,461,756 · genomes 0/152,344 · 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.Phe3010=
- Coding
- c.9030T>C
- MANE Select
- NM_000384
- dbSNP
- rs775869949
- Type
- single nucleotide variant
- Location
- chr2:21007838 (GRCh38)
- Gene constraint
- LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Similar variants
- APOB p.Arg490Trp Pathogenic/Likely pathogenic ★★ same condition
- APOB c.1124+3A>G Uncertain significance ★★ same condition
- APOB c.11788+4A>G Uncertain significance ★★ same condition
- APOB c.12087+2T>C Uncertain significance ★★ same condition
- APOB p.Ala1320Thr Uncertain significance ★★ ⚠ same condition
- APOB p.Ala1695Val Uncertain significance ★★ ⚠ same condition
- APOB p.Ala1975Ser Uncertain significance ★★ ⚠ same condition
- APOB p.Ala3008Thr Uncertain significance ★★ ⚠ 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-phe3010 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown