dbSNP rs3810153: CD79A:c.*422G>A (chr19-41881402-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001783.4(CD79A):c.*422G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 342,696 control chromosomes in the GnomAD database, including 47,642 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 18396 hom., cov: 31)

Exomes 𝑓: 0.54 ( 29246 hom. )

Consequence

CD79A
NM_001783.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.165

Publications

10 publications found

Variant links:

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: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
autosomal agammaglobulinemia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CD79A links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001783.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD79A	NM_001783.4	MANE Select	c.*422G>A		downstream_gene	N/A	NP_001774.1	P11912-1
	CD79A	NM_021601.4		c.*422G>A		downstream_gene	N/A	NP_067612.1	P11912-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD79A	ENST00000221972.8	TSL:1 MANE Select	c.*422G>A		downstream_gene	N/A	ENSP00000221972.3	P11912-1

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71188

AN:

151702

Hom.:

18393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.694

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.475

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.563

Gnomad OTH

AF:

0.517

GnomAD4 exome

AF:

0.542

AC:

103466

AN:

190876

Hom.:

29246

Cov.:

AF XY:

0.547

AC XY:

52660

AN XY:

96254

show subpopulations

African (AFR)

AF:

0.227

AC:

1830

AN:

8066

American (AMR)

AF:

0.528

AC:

4486

AN:

8500

Ashkenazi Jewish (ASJ)

AF:

0.644

AC:

4915

AN:

7628

East Asian (EAS)

AF:

0.474

AC:

7999

AN:

16892

South Asian (SAS)

AF:

0.590

AC:

11890

AN:

20148

European-Finnish (FIN)

AF:

0.554

AC:

2460

AN:

4440

Middle Eastern (MID)

AF:

0.707

AC:

631

AN:

892

European-Non Finnish (NFE)

AF:

0.559

AC:

62709

AN:

112218

Other (OTH)

AF:

0.541

AC:

6546

AN:

12092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

2230

4459

6689

8918

11148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

376

752

1128

1504

1880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.469

AC:

71199

AN:

151820

Hom.:

18396

Cov.:

AF XY:

0.473

AC XY:

35103

AN XY:

74180

show subpopulations

African (AFR)

AF:

0.230

AC:

9504

AN:

41388

American (AMR)

AF:

0.531

AC:

8110

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.638

AC:

2213

AN:

3468

East Asian (EAS)

AF:

0.476

AC:

2443

AN:

5130

South Asian (SAS)

AF:

0.583

AC:

2813

AN:

4822

European-Finnish (FIN)

AF:

0.570

AC:

6012

AN:

10548

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.563

AC:

38186

AN:

67880

Other (OTH)

AF:

0.511

AC:

1080

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1792

3584

5376

7168

8960

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

640

1280

1920

2560

3200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.527

Hom.:

24991

Bravo

AF:

0.453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.9

(source)

PhyloP100

0.17

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over