chrX-153704053-G-A

Position:

chrX-153704053-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The ENST00000345046.12(BCAP31):c.383C>T(p.Thr128Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00182 in 1,209,172 control chromosomes in the GnomAD database, including 1 homozygotes. There are 697 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). Synonymous variant affecting the same amino acid position (i.e. T128T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0014 ( 0 hom., 50 hem., cov: 24)

Exomes 𝑓: 0.0019 ( 1 hom. 647 hem. )

Consequence

BCAP31
ENST00000345046.12 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:6

Conservation

PhyloP100: 7.61

Variant links:

Genes affected

BCAP31 (HGNC:16695): (B cell receptor associated protein 31) This gene encodes a member of the B-cell receptor associated protein 31 superfamily. The encoded protein is a multi-pass transmembrane protein of the endoplasmic reticulum that is involved in the anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi and in caspase 8-mediated apoptosis. Microdeletions in this gene are associated with contiguous ABCD1/DXS1375E deletion syndrome (CADDS), a neonatal disorder. Alternative splicing of this gene results in multiple transcript variants. Two related pseudogenes have been identified on chromosome 16. [provided by RefSeq, Jan 2012]

BCAP31 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=0.022595048).

BP6

Variant X-153704053-G-A is Benign according to our data. Variant chrX-153704053-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 235341.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Likely_benign=1, Uncertain_significance=1}. Variant chrX-153704053-G-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 50 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
BCAP31	NM_001256447.2 linkuse as main transcript	c.383C>T	p.Thr128Met	missense_variant	5/8	ENST00000345046.12	NP_001243376.1
BCAP31	NM_001139457.2 linkuse as main transcript	c.584C>T	p.Thr195Met	missense_variant	5/8		NP_001132929.1
BCAP31	NM_001139441.1 linkuse as main transcript	c.383C>T	p.Thr128Met	missense_variant	5/8		NP_001132913.1
BCAP31	NM_005745.8 linkuse as main transcript	c.383C>T	p.Thr128Met	missense_variant	5/8		NP_005736.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCAP31	ENST00000345046.12 linkuse as main transcript	c.383C>T	p.Thr128Met	missense_variant	5/8	1	NM_001256447.2	ENSP00000343458	P1	P51572-1

Frequencies

GnomAD3 genomes

AF:

0.00137

AC:

154

AN:

112483

Hom.:

Cov.:

AF XY:

0.00144

AC XY:

AN XY:

34641

show subpopulations

Gnomad AFR

AF:

0.000323

Gnomad AMI

AF:

0.00438

Gnomad AMR

AF:

0.00235

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000490

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00204

Gnomad OTH

AF:

0.00267

GnomAD3 exomes

AF:

0.00138

AC:

253

AN:

183054

Hom.:

AF XY:

0.00136

AC XY:

AN XY:

67502

show subpopulations

Gnomad AFR exome

AF:

0.000304

Gnomad AMR exome

AF:

0.00117

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000433

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000255

Gnomad NFE exome

AF:

0.00246

Gnomad OTH exome

AF:

0.00133

GnomAD4 exome

AF:

0.00187

AC:

2046

AN:

1096636

Hom.:

Cov.:

AF XY:

0.00179

AC XY:

647

AN XY:

362056

show subpopulations

Gnomad4 AFR exome

AF:

0.000265

Gnomad4 AMR exome

AF:

0.00128

Gnomad4 ASJ exome

AF:

0.0000516

Gnomad4 EAS exome

AF:

0.000199

Gnomad4 SAS exome

AF:

0.0000370

Gnomad4 FIN exome

AF:

0.000198

Gnomad4 NFE exome

AF:

0.00228

Gnomad4 OTH exome

AF:

0.00126

GnomAD4 genome

AF:

0.00137

AC:

154

AN:

112536

Hom.:

Cov.:

AF XY:

0.00144

AC XY:

AN XY:

34704

show subpopulations

Gnomad4 AFR

AF:

0.000322

Gnomad4 AMR

AF:

0.00235

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000490

Gnomad4 NFE

AF:

0.00204

Gnomad4 OTH

AF:

0.00264

Alfa

AF:

0.00204

Hom.:

Bravo

AF:

0.00151

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00242

AC:

ESP6500AA

AF:

0.000261

AC:

ESP6500EA

AF:

0.00163

AC:

ExAC

AF:

0.00135

AC:

164

EpiCase

AF:

0.00213

EpiControl

AF:

0.00267

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:6

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:5

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 14, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	May 10, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2017	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -

BCAP31-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 23, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.11

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.19

.;T;T;.;T;.;T;.;T

FATHMM_MKL

Uncertain

0.82

LIST_S2

Uncertain

0.93

D;.;D;D;D;D;D;D;D

M_CAP

Pathogenic

0.41

MetaRNN

Benign

0.023

T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.49

MutationAssessor

Benign

1.9

.;L;L;.;.;.;.;.;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.62

PROVEAN

Benign

-2.1

N;N;.;.;N;N;N;N;N

REVEL

Uncertain

0.44

Sift

Uncertain

0.011

D;D;.;.;D;D;D;D;D

Sift4G

Benign

0.091

T;D;.;.;.;D;D;.;.

Polyphen

0.99

.;D;D;.;.;.;.;.;.

Vest4

0.34

MVP

0.64

MPC

1.8

ClinPred

0.042

GERP RS

4.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.14

gMVP

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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