NM_003921.5:c.694C>T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_003921.5(BCL10):c.694C>T(p.Arg232*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000374 in 1,578,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_003921.5 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL10 | ENST00000648566.1 | c.694C>T | p.Arg232* | stop_gained | Exon 3 of 3 | NM_003921.5 | ENSP00000498104.1 | |||
BCL10 | ENST00000620248.3 | c.661C>T | p.Arg221* | stop_gained | Exon 3 of 3 | 5 | ENSP00000480561.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000310 AC: 7AN: 226028Hom.: 0 AF XY: 0.0000327 AC XY: 4AN XY: 122422
GnomAD4 exome AF: 0.0000378 AC: 54AN: 1426792Hom.: 0 Cov.: 30 AF XY: 0.0000353 AC XY: 25AN XY: 707552
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
Immunodeficiency 37 Uncertain:1
This sequence change results in a premature translational stop signal in the BCL10 gene (p.Arg232*). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 2 amino acids of the BCL10 protein. This variant is present in population databases (rs376302558, ExAC 0.03%). This variant has not been reported in the literature in individuals with BCL10-related disease. 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. -
Mucosa-associated lymphoma;C0345967:Mesothelioma, malignant;C1336708:Germ cell tumor of testis;C4015195:Immunodeficiency 37;C4721532:Lymphoma, non-Hodgkin, familial Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at