chr17-63929270-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000626.4(CD79B):c.646G>C(p.Gly216Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000057 in 1,614,020 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. G216G) 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.646G>C | p.Gly216Arg | missense_variant | 6/6 | ENST00000006750.8 | |
CD79B | NM_001039933.3 | c.649G>C | p.Gly217Arg | missense_variant | 6/6 | ||
CD79B | NM_001329050.2 | c.337G>C | p.Gly113Arg | missense_variant | 5/5 | ||
CD79B | NM_021602.4 | c.334G>C | p.Gly112Arg | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD79B | ENST00000006750.8 | c.646G>C | p.Gly216Arg | missense_variant | 6/6 | 1 | NM_000626.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250770Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135606
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461794Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 727194
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.646G>C (p.G216R) alteration is located in exon 6 (coding exon 6) of the CD79B gene. This alteration results from a G to C substitution at nucleotide position 646, causing the glycine (G) at amino acid position 216 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Agammaglobulinemia 6, autosomal recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2022 | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 216 of the CD79B protein (p.Gly216Arg). This variant is present in population databases (rs777266345, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with CD79B-related conditions. ClinVar contains an entry for this variant (Variation ID: 955155). 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: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at