chrX-103309728-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032621.4(BEX2):āc.249G>Cā(p.Glu83Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 111,102 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032621.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BEX2 | NM_032621.4 | c.249G>C | p.Glu83Asp | missense_variant | 3/3 | ENST00000372677.8 | |
BEX2 | NM_001168399.2 | c.345G>C | p.Glu115Asp | missense_variant | 3/3 | ||
BEX2 | NM_001168400.2 | c.342G>C | p.Glu114Asp | missense_variant | 3/3 | ||
BEX2 | NM_001168401.2 | c.249G>C | p.Glu83Asp | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEX2 | ENST00000372677.8 | c.249G>C | p.Glu83Asp | missense_variant | 3/3 | 1 | NM_032621.4 | P1 | |
BEX2 | ENST00000536889.1 | c.345G>C | p.Glu115Asp | missense_variant | 3/3 | 2 | |||
BEX2 | ENST00000372674.5 | c.249G>C | p.Glu83Asp | missense_variant | 3/3 | 2 | P1 | ||
BEX2 | ENST00000449185.1 | c.249G>C | p.Glu83Asp | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000360 AC: 4AN: 111102Hom.: 0 Cov.: 22 AF XY: 0.0000601 AC XY: 2AN XY: 33304
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183525Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67953
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000273 AC: 3AN: 1098264Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 2AN XY: 363620
GnomAD4 genome AF: 0.0000360 AC: 4AN: 111102Hom.: 0 Cov.: 22 AF XY: 0.0000601 AC XY: 2AN XY: 33304
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at