chr11-27125776-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_003986.3(BBOX1):c.959T>G(p.Leu320Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,613,300 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 (★). Synonymous variant affecting the same amino acid position (i.e. L320L) has been classified as Likely benign.
Frequency
Consequence
NM_003986.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BBOX1 | NM_003986.3 | c.959T>G | p.Leu320Arg | missense_variant | 8/9 | ENST00000263182.8 | |
BBOX1-AS1 | NR_125768.1 | n.377+25274A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BBOX1 | ENST00000263182.8 | c.959T>G | p.Leu320Arg | missense_variant | 8/9 | 5 | NM_003986.3 | P1 | |
BBOX1-AS1 | ENST00000526061.5 | n.344+25274A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247550Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133978
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1460980Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726734
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.959T>G (p.L320R) alteration is located in exon 8 (coding exon 6) of the BBOX1 gene. This alteration results from a T to G substitution at nucleotide position 959, causing the leucine (L) at amino acid position 320 to be replaced by an arginine (R). 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