X-102154099-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001012978.3(BEX5):c.167A>G(p.Asp56Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,207,335 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012978.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000917 AC: 1AN: 109080Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 31344
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183506Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67938
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1098255Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363609
GnomAD4 genome AF: 0.00000917 AC: 1AN: 109080Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 31344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.167A>G (p.D56G) alteration is located in exon 3 (coding exon 1) of the BEX5 gene. This alteration results from a A to G substitution at nucleotide position 167, causing the aspartic acid (D) at amino acid position 56 to be replaced by a glycine (G). 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