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

CD79A links:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79A	NM_001783.4 link	c.*422G>A		downstream_gene_variant		ENST00000221972.8	NP_001774.1	P11912-1
CD79A	NM_021601.4 link	c.*422G>A		downstream_gene_variant			NP_067612.1	P11912-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD79A	ENST00000221972.8 link	c.*422G>A		downstream_gene_variant		1	NM_001783.4	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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over