19-41880705-C-T

Variant names:

• chr19-41880705-C-T
• rs367608135
• NM_001783.4:c.534C>T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001783.4(CD79A):​c.534C>T​(p.Ala178Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,295,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00098 (0 hom., cov: 28)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: CD79A NM_001783.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.179
• 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: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
• autosomal agammaglobulinemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 19-41880705-C-T is Benign according to our data. Variant chr19-41880705-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 487217.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.179 with no splicing effect.

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.534C>T	p.Ala178Ala	synonymous	Exon 4 of 5	NP_001774.1	P11912-1
	CD79A	NM_021601.4		c.420C>T	p.Ala140Ala	synonymous	Exon 4 of 5	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.534C>T	p.Ala178Ala	synonymous	Exon 4 of 5	ENSP00000221972.3	P11912-1
	CD79A	ENST00000444740.2	TSL:1	c.420C>T	p.Ala140Ala	synonymous	Exon 4 of 5	ENSP00000400605.1	P11912-2
	CD79A	ENST00000597454.2	TSL:3	c.779C>T	p.Pro260Leu	missense	Exon 3 of 4	ENSP00000468922.2	M0QX61

Frequencies

GnomAD3 genomes AF: 0.000986 AC: 138 AN: 139954 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00317

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000632

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000541

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000157

Gnomad OTH AF: 0.00101

GnomAD2 exomes AF: 0.000193 AC: 30 AN: 155430 AF XY: 0.000183

Gnomad AFR exome AF: 0.00237

Gnomad AMR exome AF: 0.000203

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000167

Gnomad OTH exome AF: 0.000228

GnomAD4 exome AF: 0.000110 AC: 127 AN: 1154922 Hom.: 0 Cov.: 33 AF XY: 0.0000865 AC XY: 49 AN XY: 566386

African (AFR) AF: 0.00388 AC: 95 AN: 24502

American (AMR) AF: 0.000212 AC: 6 AN: 28344

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15974

East Asian (EAS) AF: 0.0000764 AC: 1 AN: 13094

South Asian (SAS) AF: 0.0000389 AC: 3 AN: 77032

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4186

European-Non Finnish (NFE) AF: 0.00000977 AC: 9 AN: 921544

Other (OTH) AF: 0.000312 AC: 13 AN: 41704

GnomAD4 genome AF: 0.000978 AC: 137 AN: 140094 Hom.: 0 Cov.: 28 AF XY: 0.00115 AC XY: 78 AN XY: 67926

African (AFR) AF: 0.00314 AC: 123 AN: 39192

American (AMR) AF: 0.000631 AC: 9 AN: 14266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3288

East Asian (EAS) AF: 0.00 AC: 0 AN: 3950

South Asian (SAS) AF: 0.000538 AC: 2 AN: 3718

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8662

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 282

European-Non Finnish (NFE) AF: 0.0000157 AC: 1 AN: 63880

Other (OTH) AF: 0.000995 AC: 2 AN: 2010

Alfa AF: 0.000498 Hom.: 0

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Agammaglobulinemia 3, autosomal recessive (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.6
DANN	Benign	0.62
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

dbSNP: rs367608135; hg19: chr19-42384772;