chrX-103063171-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_018476.4(BEX1):c.104C>T(p.Ala35Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000423 in 1,209,789 control chromosomes in the GnomAD database, including 1 homozygotes. There are 179 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018476.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BEX1 | NM_018476.4 | c.104C>T | p.Ala35Val | missense_variant | 3/3 | ENST00000372728.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEX1 | ENST00000372728.4 | c.104C>T | p.Ala35Val | missense_variant | 3/3 | 1 | NM_018476.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000215 AC: 24AN: 111536Hom.: 0 Cov.: 22 AF XY: 0.0000890 AC XY: 3AN XY: 33726
GnomAD3 exomes AF: 0.000218 AC: 40AN: 183199Hom.: 0 AF XY: 0.000251 AC XY: 17AN XY: 67697
GnomAD4 exome AF: 0.000444 AC: 488AN: 1098201Hom.: 1 Cov.: 31 AF XY: 0.000484 AC XY: 176AN XY: 363555
GnomAD4 genome ? AF: 0.000215 AC: 24AN: 111588Hom.: 0 Cov.: 22 AF XY: 0.0000888 AC XY: 3AN XY: 33788
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.104C>T (p.A35V) alteration is located in exon 3 (coding exon 1) of the BEX1 gene. This alteration results from a C to T substitution at nucleotide position 104, causing the alanine (A) at amino acid position 35 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | BEX1: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at