Is APOBEC3B p.Arg211Trp (c.631C>T) pathogenic?

APOBEC3B p.Arg211Trp (c.631C>T) is classified Likely benign in APOBEC3B (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely benign (0.1746); Ultra-rare (popmax 0.0818%, amr).

How common is APOBEC3B p.Arg211Trp (c.631C>T) in the general population?

APOBEC3B p.Arg211Trp (c.631C>T) is ultra-rare (popmax 0.0818%, amr) (gnomAD).

What do computational predictors say about APOBEC3B p.Arg211Trp (c.631C>T)?

AlphaMissense predicts likely benign (score 0.1746) — an in-silico prediction, not a clinical call.

APOBEC3B p.Arg211Trp

c.631C>T · rs200770515 · VCV1048995

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1746 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0818%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1746	likely benign
REVEL	0.139	moderately benign-leaning
SaProt	LLR -9.17	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.29 · evaluated, not missing
Constraint at this position
Conservation	phyloP -15	GERP -3.4
Regional constraint	o/e 0.94	unconstrained · MANE · 3,632 bp · p 0.41 · regional, not allelic
Overall
CADD	13.53	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 0.0818% Admixed American · 46/56,242 alleles

Filtering AF 0.0629% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0564%

Overall 0.0378% 601/1,588,646 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0818%	1,223
European (non-Finnish)	0.045%	2,223
Remaining individualsnot grpmax-eligible	0.0262%	3,820
African / African-American	0.00808%	12,377
Finnishnot grpmax-eligible	0.00634%	15,782
South Asian	0.00339%	29,473

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: APOBEC3B
Protein: p.Arg211Trp
Coding: c.631C>T
MANE Select: NM_004900
dbSNP: rs200770515
Type: single nucleotide variant
Location: chr22:38989518 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.94 · 13 PDB
Residue 211: the cmp/dcmp-type deaminase 2 domain

Full APOBEC3B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

APOBEC3B p.Asn23= Benign ★★ same type
APOBEC3B p.Pro206= Benign ★★ same type
APOBEC3B c.174+1G>T Uncertain significance ★ same type
APOBEC3B p.Ala242Ser Uncertain significance ★ ⚠ same type
APOBEC3B p.Ala331Ser Uncertain significance ★ ⚠ same type
APOBEC3B p.Ala375Val Uncertain significance ★ ⚠ same type
APOBEC3B p.Arg183Cys Uncertain significance ★ ⚠ same type
APOBEC3B p.Arg212Leu 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/apobec3b-p-arg211trp (accessed [today's date]).

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