Is BMF p.Ser77Thr (c.229T>A) pathogenic?

BMF p.Ser77Thr (c.229T>A) is classified Uncertain significance in BMF (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-11). AlphaMissense: likely benign (0.1232); Absent from gnomAD v4.1.

How common is BMF p.Ser77Thr (c.229T>A) in the general population?

BMF p.Ser77Thr (c.229T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BMF p.Ser77Thr (c.229T>A)?

AlphaMissense predicts likely benign (score 0.1232) — an in-silico prediction, not a clinical call.

BMF p.Ser77Thr

c.229T>A · rs2504862596 · VCV2610791

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1232 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1232	likely benign
REVEL	0.202	benign-leaning
SaProt	LLR -7.03	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.1	GERP 2.1, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 14 kb · p 0.17 · regional, not allelic
Overall
CADD	23.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BMF
Protein: p.Ser77Thr
Coding: c.229T>A
MANE Select: NM_001003940
dbSNP: rs2504862596
Type: single nucleotide variant
Location: chr15:40105858 (GRCh38)
Gene constraint: LOEUF 0.788 · pLI 0.10 (gnomAD)
Structure: AlphaFold pLDDT 62.81 · 5 PDB

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

Similar variants

BMF p.Ala100Thr Uncertain significance ★ ⚠ same type
BMF p.Ala171Thr Uncertain significance ★ ⚠ same type
BMF p.Arg103Leu Uncertain significance ★ ⚠ same type
BMF p.Arg135Gln Uncertain significance ★ ⚠ same type
BMF p.Arg94Gln Uncertain significance ★ ⚠ same type
BMF p.Asp12Asn Uncertain significance ★ ⚠ same type
BMF p.Gln16His Uncertain significance ★ ⚠ same type
BMF p.Glu118Val 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/bmf-p-ser77thr (accessed [today's date]).

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