chr11-122977684-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001098169.2(BSX):c.667G>C(p.Glu223Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000869 in 1,611,752 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. E223E) has been classified as Likely benign.
Frequency
Consequence
NM_001098169.2 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 |
---|---|---|---|---|---|---|---|
BSX | NM_001098169.2 | c.667G>C | p.Glu223Gln | missense_variant | 3/3 | ENST00000343035.3 | |
LOC124902774 | XR_007062926.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BSX | ENST00000343035.3 | c.667G>C | p.Glu223Gln | missense_variant | 3/3 | 5 | NM_001098169.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 244918Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133406
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1459524Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726208
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.667G>C (p.E223Q) alteration is located in exon 3 (coding exon 3) of the BSX gene. This alteration results from a G to C substitution at nucleotide position 667, causing the glutamic acid (E) at amino acid position 223 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at