Is CD79B p.Asn37His (c.109A>C) pathogenic?

CD79B p.Asn37His (c.109A>C) is classified Uncertain significance in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-20). AlphaMissense: likely benign (0.1477); Very rare (popmax 8.47e-05%, nfe).

How common is CD79B p.Asn37His (c.109A>C) in the general population?

CD79B p.Asn37His (c.109A>C) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

What do computational predictors say about CD79B p.Asn37His (c.109A>C)?

AlphaMissense predicts likely benign (score 0.1477) — an in-silico prediction, not a clinical call.

CD79B p.Asn37His

c.109A>C · VCV3264876

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1477 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1477	likely benign
REVEL	0.236	benign-leaning
SaProt	LLR -6.61	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 0.075	GERP -3.5
Regional constraint	o/e 0.73	unconstrained · MANE · 3,032 bp · p 2.7e-06 · regional, not allelic
Overall
CADD	10.68	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 8.47e-05% European (non-Finnish) · 1/1,179,998 alleles

Overall 6.84e-05% 1/1,461,672 alleles · very rare

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.Asn37His
Coding: c.109A>C
MANE Select: NM_000626
Type: single nucleotide variant
Location: chr17:63931344 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB

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-asn37his (accessed [today's date]).

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