FLNB p.Ser2496=
c.7488G>A · rs539241620 · VCV2202982
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.103%, sas)
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 -1.9 | GERP -5.7 |
| Overall | ||
| CADD | 8.326 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
South Asian · 94/91,072 alleles
Filtering AF
0.0863%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.08%
Overall
0.0083%
134/1,613,928 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.103% | 969 |
| Admixed American | 0.01% | 10,004 |
| East Asian | 0.00891% | 11,220 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,831 |
| European (non-Finnish) | 0.0022% | 45,379 |
| African / African-American | 0.00133% | 74,988 |
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
- FLNB
- Protein
- p.Ser2496=
- Coding
- c.7488G>A
- MANE Select
- NM_001457
- dbSNP
- rs539241620
- Type
- single nucleotide variant
- Location
- chr3:58169660 (GRCh38)
- Gene constraint
- LOEUF 0.504 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.96 · 23 PDB
- Residue 2496
- the 'interaction with inppl1' region; the 'self-association site, tail' region; the 'hinge 2' region
Similar variants
- FLNB p.Ser2496Trp Uncertain significance ★★ ⚠ same residue
- FLNB p.Ser2496Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- FLNB c.4390+2T>C Pathogenic/Likely pathogenic ★★ same type
- FLNB c.5110-1G>A Likely pathogenic ★★ same type
- FLNB p.Arg1463Ter Pathogenic/Likely pathogenic ★★ same type
- FLNB p.Arg1948Ter Pathogenic ★★ same type
- FLNB p.Arg649Ter Pathogenic ★★ same type
- FLNB p.Asp167Gly Likely 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/flnb-p-ser2496 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown