NM_001783.4:c.83C>G

Variant names:

• chr19-41878993-C-G
• NM_001783.4:c.83C>G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001783.4(CD79A):​c.83C>G​(p.Pro28Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: CD79A NM_001783.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.96
• Publications: 0 publications found

Genes affected

CD79A (HGNC:1698): (CD79a molecule) The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-alpha protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

CD79A Gene-Disease associations (from GenCC):

• agammaglobulinemia 3, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
• autosomal agammaglobulinemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.35133606).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79A	NM_001783.4	c.83C>G	p.Pro28Arg	missense_variant	Exon 2 of 5	ENST00000221972.8	NP_001774.1
CD79A	NM_021601.4	c.83C>G	p.Pro28Arg	missense_variant	Exon 2 of 5		NP_067612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD79A	ENST00000221972.8	c.83C>G	p.Pro28Arg	missense_variant	Exon 2 of 5	1	NM_001783.4	ENSP00000221972.3
CD79A	ENST00000444740.2	c.83C>G	p.Pro28Arg	missense_variant	Exon 2 of 5	1		ENSP00000400605.1
CD79A	ENST00000597454.2	c.83C>G	p.Pro28Arg	missense_variant	Exon 2 of 4	3		ENSP00000468922.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 10, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.83C>G (p.P28R) alteration is located in exon 2 (coding exon 2) of the CD79A gene. This alteration results from a C to G substitution at nucleotide position 83, causing the proline (P) at amino acid position 28 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.015	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.54	D;T;.
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.29
FATHMM_MKL	Benign	0.67	D
LIST_S2	Benign	0.75	T;T;T
M_CAP	Benign	0.028	D
MetaRNN	Benign	0.35	T;T;T
MetaSVM	Benign	-0.51	T
MutationAssessor	Benign	1.0	L;.;L
PhyloP100		4.0
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-2.0	N;.;D
REVEL	Uncertain	0.35
Sift	Benign	0.081	T;.;D
Sift4G	Uncertain	0.056	T;D;D
Polyphen		1.0	D;.;.
Vest4		0.51
MutPred		0.54		Gain of catalytic residue at P28 (P = 0.0172);Gain of catalytic residue at P28 (P = 0.0172);Gain of catalytic residue at P28 (P = 0.0172);
MVP		0.68
MPC		1.2
ClinPred		0.88	D
GERP RS		4.5
Varity_R		0.097
gMVP		0.34
Mutation Taster		=75/25	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

hg19: chr19-42383063;