Variant X-103310417-C-T details in Genebe, Genetics Data Aggregator

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: 𝑓 0.0016 ( 0 hom., 58 hem., cov: 23)

Exomes 𝑓: 0.00015 ( 1 hom. 34 hem. )

Consequence

BEX2
NM_032621.4 5_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.943

Variant links:

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]

BEX2 links:

Genome browser will be placed here

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
BEX2	NM_032621.4 linkuse as main transcript	c.-65G>A		5_prime_UTR_variant	2/3	ENST00000372677.8
BEX2	NM_001168399.2 linkuse as main transcript	c.32G>A	p.Cys11Tyr	missense_variant	2/3
BEX2	NM_001168400.2 linkuse as main transcript	c.29G>A	p.Cys10Tyr	missense_variant	2/3
BEX2	NM_001168401.2 linkuse as main transcript	c.-65G>A		5_prime_UTR_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BEX2	ENST00000372677.8 linkuse as main transcript	c.-65G>A		5_prime_UTR_variant	2/3	1	NM_032621.4	P1	Q9BXY8-1
BEX2	ENST00000536889.1 linkuse as main transcript	c.32G>A	p.Cys11Tyr	missense_variant	2/3	2			Q9BXY8-2
BEX2	ENST00000372674.5 linkuse as main transcript	c.-65G>A		5_prime_UTR_variant	2/3	2		P1	Q9BXY8-1
BEX2	ENST00000449185.1 linkuse as main transcript	c.-65G>A		5_prime_UTR_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.00158

AC:

178

AN:

112779

Hom.:

Cov.:

AF XY:

0.00166

AC XY:

AN XY:

34927

show subpopulations

Gnomad AFR

AF:

0.00550

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000648

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000417

AC:

AN:

103207

Hom.:

AF XY:

0.000294

AC XY:

AN XY:

37363

show subpopulations

Gnomad AFR exome

AF:

0.00591

Gnomad AMR exome

AF:

0.000310

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000319

GnomAD4 exome

AF:

0.000151

AC:

158

AN:

1042951

Hom.:

Cov.:

AF XY:

0.0000996

AC XY:

AN XY:

341463

show subpopulations

Gnomad4 AFR exome

AF:

0.00502

Gnomad4 AMR exome

AF:

0.000394

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000122

Gnomad4 OTH exome

AF:

0.000452

GnomAD4 genome

AF:

0.00157

AC:

177

AN:

112829

Hom.:

Cov.:

AF XY:

0.00166

AC XY:

AN XY:

34987

show subpopulations

Gnomad4 AFR

AF:

0.00546

Gnomad4 AMR

AF:

0.000647

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000953

Hom.:

Bravo

AF:

0.00172

ExAC

AF:

0.000653

AC:

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.0

DANN

Benign

0.53

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.44

M_CAP

Benign

0.0050

MetaRNN

Benign

0.0043

MetaSVM

Benign

-0.98

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Uncertain

0.55

PROVEAN

Benign

-1.1

REVEL

Benign

0.053

Sift

Uncertain

0.021

Sift4G

Benign

0.092

Vest4

0.34

MVP

0.043

MPC

0.37

ClinPred

0.012

GERP RS

0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

gMVP

0.034

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over