chr17-63929281-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000626.4(CD79B):c.635C>T(p.Thr212Met) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,613,884 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T212T) has been classified as Likely benign.
Frequency
Consequence
NM_000626.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD79B | NM_000626.4 | c.635C>T | p.Thr212Met | missense_variant | 6/6 | ENST00000006750.8 | |
CD79B | NM_001039933.3 | c.638C>T | p.Thr213Met | missense_variant | 6/6 | ||
CD79B | NM_001329050.2 | c.326C>T | p.Thr109Met | missense_variant | 5/5 | ||
CD79B | NM_021602.4 | c.323C>T | p.Thr108Met | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD79B | ENST00000006750.8 | c.635C>T | p.Thr212Met | missense_variant | 6/6 | 1 | NM_000626.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250802Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135614
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461724Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727166
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
Agammaglobulinemia 6, autosomal recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2020 | 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. 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with CD79B-related disease. This variant is present in population databases (rs149266494, ExAC 0.01%). This sequence change replaces threonine with methionine at codon 212 of the CD79B protein (p.Thr212Met). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and methionine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at