X-103063024-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018476.4(BEX1):c.251G>A(p.Arg84Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000926 in 1,209,322 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 36 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 (★).
Frequency
Consequence
NM_018476.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 54AN: 111003Hom.: 0 Cov.: 22 AF XY: 0.000543 AC XY: 18AN XY: 33167
GnomAD3 exomes AF: 0.000153 AC: 28AN: 183532Hom.: 0 AF XY: 0.000118 AC XY: 8AN XY: 67960
GnomAD4 exome AF: 0.0000528 AC: 58AN: 1098265Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 18AN XY: 363619
GnomAD4 genome AF: 0.000486 AC: 54AN: 111057Hom.: 0 Cov.: 22 AF XY: 0.000542 AC XY: 18AN XY: 33231
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.251G>A (p.R84K) alteration is located in exon 3 (coding exon 1) of the BEX1 gene. This alteration results from a G to A substitution at nucleotide position 251, causing the arginine (R) at amino acid position 84 to be replaced by a lysine (K). 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