Is BAD p.Asp82Glu (c.246C>G) pathogenic?

BAD p.Asp82Glu (c.246C>G) is classified Likely benign in BAD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-16). AlphaMissense: likely benign (0.0609); Rare (popmax 0.13%, amr).

How common is BAD p.Asp82Glu (c.246C>G) in the general population?

BAD p.Asp82Glu (c.246C>G) is rare (popmax 0.13%, amr) (gnomAD).

What do computational predictors say about BAD p.Asp82Glu (c.246C>G)?

AlphaMissense predicts likely benign (score 0.0609) — an in-silico prediction, not a clinical call.

BAD p.Asp82Glu

c.246C>G · rs145689917 · VCV2459152

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0609 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.13%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0609	likely benign
REVEL	0.024	moderately benign-leaning
SaProt	LLR -4.98	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 -1.8	GERP -2.1
Regional constraint	o/e 1.23	unconstrained · MANE · 14 kb · p 0.0004 · regional, not allelic
Overall
CADD	1.86	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.13% Admixed American · 47/36,110 alleles

Filtering AF 0.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.09%

Overall 0.00851% 123/1,446,168 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.13%	768
African / African-American	0.082%	1,220
Remaining individualsnot grpmax-eligible	0.02%	4,999
Middle Eastern	0.0187%	5,354
European (non-Finnish)	0.000727%	137,464

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: BAD
Protein: p.Asp82Glu
Coding: c.246C>G
MANE Select: NM_032989
dbSNP: rs145689917
Type: single nucleotide variant
Location: chr11:64271745 (GRCh38)
Gene constraint: LOEUF 1.889 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.91 · 6 PDB
Residue 82: the 'disordered' region

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

Similar variants

BAD p.Asp82Asn Uncertain significance ★ ⚠ same residue
BAD p.Ala106Val Uncertain significance ★ ⚠ same type
BAD p.Ala138Thr Uncertain significance ★ ⚠ same type
BAD p.Ala41Thr Uncertain significance ★ ⚠ same type
BAD p.Arg116Ser Uncertain significance ★ ⚠ same type
BAD p.Arg161Gly Uncertain significance ★ ⚠ same type
BAD p.Gln152Arg Uncertain significance ★ ⚠ same type
BAD p.Glu81Gln 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/bad-p-asp82glu (accessed [today's date]).

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