Is BID p.Ser96Asn (c.287G>A) pathogenic?

BID p.Ser96Asn (c.287G>A) is classified Uncertain significance in BID (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). AlphaMissense: likely benign (0.1143); Very rare (popmax 0.00167%, amr).

How common is BID p.Ser96Asn (c.287G>A) in the general population?

BID p.Ser96Asn (c.287G>A) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about BID p.Ser96Asn (c.287G>A)?

AlphaMissense predicts likely benign (score 0.1143) — an in-silico prediction, not a clinical call.

BID p.Ser96Asn

c.287G>A · VCV4208820

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1143 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1143	likely benign
REVEL	0.076	moderately benign-leaning
SaProt	LLR -6.18	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 -0.067	GERP -1.3
Regional constraint	o/e 0.88	unconstrained · MANE · 15 kb · p 0.061 · regional, not allelic
Overall
CADD	8.497	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

Grpmax group 0.00167% Admixed American · 1/60,004 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000434% 7/1,612,192 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,004
Remaining individualsnot grpmax-eligible	0.0016%	62,468
European (non-Finnish)	0.000424%	235,982

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: BID
Protein: p.Ser96Asn
Coding: c.287G>A
MANE Select: NM_001196
Type: single nucleotide variant
Location: chr22:17739425 (GRCh38)
Gene constraint: LOEUF 1.553 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.12 · 17 PDB
Residue 96: an α-helix

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

Similar variants

BID c.-14G>A Uncertain significance ★ same type
BID c.-15C>T Uncertain significance ★ same type
BID c.-23G>A Uncertain significance ★ same type
BID c.-24C>G Uncertain significance ★ same type
BID c.-33G>A Uncertain significance ★ same type
BID c.-39G>A Uncertain significance ★ same type
BID c.-59+698A>G Uncertain significance ★ same type
BID c.-59+722C>T 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/bid-p-ser96asn (accessed [today's date]).

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