rs532288711
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001783.4(CD79A):āc.593T>Cā(p.Met198Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00027 in 1,605,722 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00012 ( 0 hom., cov: 31)
Exomes š: 0.00029 ( 1 hom. )
Consequence
CD79A
NM_001783.4 missense
NM_001783.4 missense
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 4.17
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3444494).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD79A | NM_001783.4 | c.593T>C | p.Met198Thr | missense_variant | 5/5 | ENST00000221972.8 | |
CD79A | NM_021601.4 | c.479T>C | p.Met160Thr | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD79A | ENST00000221972.8 | c.593T>C | p.Met198Thr | missense_variant | 5/5 | 1 | NM_001783.4 | P1 | |
CD79A | ENST00000444740.2 | c.479T>C | p.Met160Thr | missense_variant | 5/5 | 1 | |||
CD79A | ENST00000597454.2 | c.*19T>C | 3_prime_UTR_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000119 AC: 18AN: 151870Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000149 AC: 35AN: 235186Hom.: 1 AF XY: 0.000158 AC XY: 20AN XY: 126970
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GnomAD4 exome AF: 0.000286 AC: 416AN: 1453734Hom.: 1 Cov.: 31 AF XY: 0.000274 AC XY: 198AN XY: 722200
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GnomAD4 genome ? AF: 0.000118 AC: 18AN: 151988Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74286
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Agammaglobulinemia 3, autosomal recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 23, 2022 | This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 198 of the CD79A protein (p.Met198Thr). This variant is present in population databases (rs532288711, gnomAD 0.03%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with CD79A-related conditions. ClinVar contains an entry for this variant (Variation ID: 133837). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
P;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at