Is CD79A p.Val157Ala (c.470T>C) pathogenic?

CD79A p.Val157Ala (c.470T>C) is classified Uncertain significance in CD79A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-06). AlphaMissense: ambiguous (0.5441); Very rare (popmax 0.000679%, nfe).

How common is CD79A p.Val157Ala (c.470T>C) in the general population?

CD79A p.Val157Ala (c.470T>C) is very rare (popmax 0.000679%, nfe) (gnomAD).

What do computational predictors say about CD79A p.Val157Ala (c.470T>C)?

AlphaMissense predicts ambiguous (score 0.5441) — an in-silico prediction, not a clinical call.

CD79A p.Val157Ala

c.470T>C · VCV4223034

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5441 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000679%, nfe)

Computational evidence

Protein change
AlphaMissense	0.5441	ambiguous
REVEL	0.371	indeterminate
SaProt	LLR -6.33	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.5, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 3,672 bp · p 0.00029 · regional, not allelic
Overall
CADD	23.2	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 0.000679% European (non-Finnish) · 8/1,178,678 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000496% 8/1,611,330 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: CD79A
Protein: p.Val157Ala
Coding: c.470T>C
MANE Select: NM_001783
Type: single nucleotide variant
Location: chr19:41879625 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 157: an α-helix

Full CD79A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD79A p.Val157Met Uncertain significance ★ same residue
CD79A p.Arg124Cys Uncertain significance ★★ ⚠ same type
CD79A p.Arg124His Uncertain significance ★★ ⚠ same type
CD79A p.Arg168Gln Uncertain significance ★★ same type
CD79A p.Arg204Gln Uncertain significance ★★ ⚠ same type
CD79A p.Asn60Ser Uncertain significance ★★ ⚠ same type
CD79A p.Asn63Ser Uncertain significance ★★ ⚠ same type
CD79A p.Gly179Arg 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/cd79a-p-val157ala (accessed [today's date]).

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