Is CD79B c.*89T>C pathogenic?

CD79B c.89T>C is classified Benign in CD79B (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-01-24). Common (popmax 68.7%, mid) — too common for a highly-penetrant pathogenic allele.

CD79B c.*89T>C

Q: How common is CD79B c.*89T>C in the general population?

CD79B c.*89T>C is common (popmax 68.7%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs1051684 · VCV1287682

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 68.7%, mid) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.80 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.17	GERP -2.4
Non-coding constraint	Z 1.75	1 kb window · o/e 0.82 · regional · uncalibrated
Overall
CADD	2.102	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 68.7% Middle Eastern · 2,301/3,348 alleles

Filtering AF 66.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 66.4%

Overall 62% 556,222/897,194 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	76.5%	1
Middle Easterngrpmax	68.7%	1
Ashkenazi Jewishnot grpmax-eligible	67.3%	1
African / African-American	67.2%	1
European (non-Finnish)	66.1%	2
Remaining individualsnot grpmax-eligible	62.4%	2
Finnishnot grpmax-eligible	58.8%	2
Admixed American	50.8%	2
East Asian	46.3%	2
South Asian	46%	2

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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
Coding: c.*89T>C
MANE Select: NM_000626
dbSNP: rs1051684
Type: single nucleotide variant
Location: chr17:63929137 (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-c-star-89t-c (accessed [today's date]).

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