chrX-103063225-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_018476.4(BEX1):c.50C>A(p.Ala17Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,209,237 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A17V) has been classified as Likely benign.
Frequency
Consequence
NM_018476.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BEX1 | NM_018476.4 | c.50C>A | p.Ala17Asp | missense_variant | 3/3 | ENST00000372728.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEX1 | ENST00000372728.4 | c.50C>A | p.Ala17Asp | missense_variant | 3/3 | 1 | NM_018476.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000270 AC: 3AN: 111234Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33450
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182447Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67241
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1098003Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363359
GnomAD4 genome ? AF: 0.0000270 AC: 3AN: 111234Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.50C>A (p.A17D) alteration is located in exon 3 (coding exon 1) of the BEX1 gene. This alteration results from a C to A substitution at nucleotide position 50, causing the alanine (A) at amino acid position 17 to be replaced by an aspartic acid (D). 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