Is CD79B p.Gly72Ser (c.214G>A) pathogenic?

CD79B p.Gly72Ser (c.214G>A) is classified Likely benign in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-20). AlphaMissense: likely benign (0.0755); Ultra-rare (popmax 0.0133%, afr).

How common is CD79B p.Gly72Ser (c.214G>A) in the general population?

CD79B p.Gly72Ser (c.214G>A) is ultra-rare (popmax 0.0133%, afr) (gnomAD).

What do computational predictors say about CD79B p.Gly72Ser (c.214G>A)?

AlphaMissense predicts likely benign (score 0.0755) — an in-silico prediction, not a clinical call.

CD79B p.Gly72Ser

c.214G>A · rs373078798 · VCV3140670

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0755 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0755	likely benign
REVEL	0.136	moderately benign-leaning
SaProt	LLR -8.67	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 -0.61	GERP -4.3
Regional constraint	o/e 0.73	unconstrained · MANE · 3,032 bp · p 2.7e-06 · regional, not allelic
Overall
CADD	1.788	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 0.0133% African / African-American · 10/75,052 alleles

Filtering AF 0.00722% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00549%

Overall 0.00192% 31/1,614,210 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0133%	7,505
East Asian	0.0111%	8,979
Admixed American	0.005%	20,009
South Asian	0.0011%	91,084
European (non-Finnish)	0.00102%	98,335

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: CD79B
Protein: p.Gly72Ser
Coding: c.214G>A
MANE Select: NM_000626
dbSNP: rs373078798
Type: single nucleotide variant
Location: chr17:63930290 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 72: a disulfide bond; a β-strand; the ig-like v-type domain

Full CD79B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD79B p.Ala5Val Uncertain significance ★★ ⚠ same type
CD79B p.Arg36Trp Uncertain significance ★★ ⚠ same type
CD79B p.Gly216Arg Uncertain significance ★★ ⚠ same type
CD79B p.Leu91Pro Uncertain significance ★★ ⚠ same type
CD79B p.Met96Val Uncertain significance ★★ ⚠ same type
CD79B p.Thr212Met Uncertain significance ★★ ⚠ same type
CD79B p.Val175Met Uncertain significance ★★ ⚠ same type
CD79B c.118+12C>T Benign/Likely benign ★★ 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/cd79b-p-gly72ser (accessed [today's date]).

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