19-41879044-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001783.4(CD79A):āc.134G>Cā(p.Ser45Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,613,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_001783.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD79A | NM_001783.4 | c.134G>C | p.Ser45Thr | missense_variant | 2/5 | ENST00000221972.8 | NP_001774.1 | |
CD79A | NM_021601.4 | c.134G>C | p.Ser45Thr | missense_variant | 2/5 | NP_067612.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD79A | ENST00000221972.8 | c.134G>C | p.Ser45Thr | missense_variant | 2/5 | 1 | NM_001783.4 | ENSP00000221972.3 | ||
CD79A | ENST00000444740.2 | c.134G>C | p.Ser45Thr | missense_variant | 2/5 | 1 | ENSP00000400605.1 | |||
CD79A | ENST00000597454.2 | c.134G>C | p.Ser45Thr | missense_variant | 2/4 | 3 | ENSP00000468922.2 |
Frequencies
GnomAD3 genomes AF: 0.000244 AC: 37AN: 151888Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000147 AC: 37AN: 250858Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135724
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461064Hom.: 0 Cov.: 36 AF XY: 0.0000715 AC XY: 52AN XY: 726840
GnomAD4 genome AF: 0.000243 AC: 37AN: 152006Hom.: 0 Cov.: 31 AF XY: 0.000202 AC XY: 15AN XY: 74320
ClinVar
Submissions by phenotype
Agammaglobulinemia 3, autosomal recessive Uncertain:4
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 05, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Oct 07, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 05, 2022 | This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 45 of the CD79A protein (p.Ser45Thr). This variant is present in population databases (rs199603062, gnomAD 0.07%). 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: 839358). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 31, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at