chrX-103310417-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032621.4(BEX2):​c.-65G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,155,780 control chromosomes in the GnomAD database, including 1 homozygotes. There are 92 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: đť‘“ 0.0016 ( 0 hom., 58 hem., cov: 23)
Exomes đť‘“: 0.00015 ( 1 hom. 34 hem. )
Consequence
BEX2
NM_032621.4 5_prime_UTR
NM_032621.4 5_prime_UTR
Scores
2
12
Clinical Significance
Conservation
PhyloP100: 0.943
Genes affected
BEX2 (HGNC:30933): (brain expressed X-linked 2) This gene belongs to the brain expressed X-linked gene family. The encoded protein interacts with the transcription factor LIM domain only 2 in a DNA-binding complex that recognizes the E-box element and promotes transcription. This gene has been found to be a tumor suppressor that is silenced in human glioma. In breast cancer cells, this gene product modulates apoptosis in response to estrogen and tamoxifen, and enhances the anti-proliferative effect of tamoxifen. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.004293382).
BP6
Variant X-103310417-C-T is Benign according to our data. Variant chrX-103310417-C-T is described in ClinVar as [Benign]. Clinvar id is 208895.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Hemizygotes in GnomAd4 at 58 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BEX2 | NM_032621.4 | c.-65G>A | 5_prime_UTR_variant | 2/3 | ENST00000372677.8 | ||
BEX2 | NM_001168399.2 | c.32G>A | p.Cys11Tyr | missense_variant | 2/3 | ||
BEX2 | NM_001168400.2 | c.29G>A | p.Cys10Tyr | missense_variant | 2/3 | ||
BEX2 | NM_001168401.2 | c.-65G>A | 5_prime_UTR_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEX2 | ENST00000372677.8 | c.-65G>A | 5_prime_UTR_variant | 2/3 | 1 | NM_032621.4 | P1 | ||
BEX2 | ENST00000536889.1 | c.32G>A | p.Cys11Tyr | missense_variant | 2/3 | 2 | |||
BEX2 | ENST00000372674.5 | c.-65G>A | 5_prime_UTR_variant | 2/3 | 2 | P1 | |||
BEX2 | ENST00000449185.1 | c.-65G>A | 5_prime_UTR_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00158 AC: 178AN: 112779Hom.: 0 Cov.: 23 AF XY: 0.00166 AC XY: 58AN XY: 34927
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GnomAD3 exomes AF: 0.000417 AC: 43AN: 103207Hom.: 1 AF XY: 0.000294 AC XY: 11AN XY: 37363
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GnomAD4 exome AF: 0.000151 AC: 158AN: 1042951Hom.: 1 Cov.: 31 AF XY: 0.0000996 AC XY: 34AN XY: 341463
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GnomAD4 genome AF: 0.00157 AC: 177AN: 112829Hom.: 0 Cov.: 23 AF XY: 0.00166 AC XY: 58AN XY: 34987
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Abnormality of neuronal migration Benign:1
Benign, no assertion criteria provided | clinical testing | Génétique et pathophysiologie de maladies neurodéveloppementales et épileptogènes, Institut de génétique et de biologie moléculaire et cellulaire | Oct 31, 2014 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at