Is FLI1 p.Ser84= (c.252C>T) pathogenic?

FLI1 p.Ser84= (c.252C>T) is classified Likely benign in FLI1 (ClinVar, Single submitter, 2 submitters; last evaluated 2022-03-23). Very rare (popmax 0.00401%, afr).

How common is FLI1 p.Ser84= (c.252C>T) in the general population?

FLI1 p.Ser84= (c.252C>T) is very rare (popmax 0.00401%, afr) (gnomAD).

FLI1 p.Ser84=

c.252C>T · rs146694829 · VCV3046224

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

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 -6.9	GERP -3.9
Overall
CADD	1.548	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00401% African / African-American · 3/74,888 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.00105% 17/1,613,296 alleles · very rare exomes 12/1,461,198 · genomes 5/152,098 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00401%	24,963
Admixed American	0.00334%	29,963
South Asian	0.0022%	45,497
European (non-Finnish)	0.000848%	117,961

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: FLI1
Protein: p.Ser84=
Coding: c.252C>T
MANE Select: NM_002017
dbSNP: rs146694829
Type: single nucleotide variant
Location: chr11:128768139 (GRCh38)
Gene constraint: LOEUF 0.367 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.32 · 14 PDB

Full FLI1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FLI1 p.Ser84Arg Uncertain significance ★ ⚠ same residue
FLI1 p.Ala178Thr Uncertain significance ★★ ⚠ same type
FLI1 p.Ala247Thr Uncertain significance ★★ ⚠ same type
FLI1 p.Ala295Ser Uncertain significance ★★ ⚠ same type
FLI1 p.Ala419Thr Uncertain significance ★★ ⚠ same type
FLI1 p.Arg177His Uncertain significance ★★ ⚠ same type
FLI1 p.Arg177Pro Uncertain significance ★★ ⚠ same type
FLI1 p.Arg257Gln 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/fli1-p-ser84 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown