Variant chrX-153700972-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001256447.2(BCAP31):c.706G>A(p.Ala236Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000756 in 1,204,975 control chromosomes in the GnomAD database, including 5 homozygotes. There are 325 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00099 ( 0 hom., 61 hem., cov: 22)

Exomes 𝑓: 0.00073 ( 5 hom. 264 hem. )

Consequence

BCAP31
NM_001256447.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0140

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0031683147).

BP6

Variant X-153700972-C-T is Benign according to our data. Variant chrX-153700972-C-T is described in ClinVar as [Benign]. Clinvar id is 2414137.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 61 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
BCAP31	NM_001256447.2 linkuse as main transcript	c.706G>A	p.Ala236Thr	missense_variant	8/8	ENST00000345046.12
BCAP31	NM_001139457.2 linkuse as main transcript	c.907G>A	p.Ala303Thr	missense_variant	8/8
BCAP31	NM_001139441.1 linkuse as main transcript	c.706G>A	p.Ala236Thr	missense_variant	8/8
BCAP31	NM_005745.8 linkuse as main transcript	c.706G>A	p.Ala236Thr	missense_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAP31	ENST00000345046.12 linkuse as main transcript	c.706G>A	p.Ala236Thr	missense_variant	8/8	1	NM_001256447.2	P1	P51572-1

Frequencies

GnomAD3 genomes

AF:

0.000995

AC:

111

AN:

111545

Hom.:

Cov.:

AF XY:

0.00181

AC XY:

AN XY:

33737

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0161

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000264

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00193

AC:

334

AN:

173362

Hom.:

AF XY:

0.00188

AC XY:

112

AN XY:

59530

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0196

Gnomad NFE exome

AF:

0.000245

Gnomad OTH exome

AF:

0.00189

GnomAD4 exome

AF:

0.000732

AC:

800

AN:

1093378

Hom.:

Cov.:

AF XY:

0.000734

AC XY:

264

AN XY:

359660

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0178

Gnomad4 NFE exome

AF:

0.0000560

Gnomad4 OTH exome

AF:

0.000719

GnomAD4 genome

AF:

0.000995

AC:

111

AN:

111597

Hom.:

Cov.:

AF XY:

0.00180

AC XY:

AN XY:

33799

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0161

Gnomad4 NFE

AF:

0.000264

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000864

Hom.:

Bravo

AF:

0.0000529

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000595

AC:

ExAC

AF:

0.00136

AC:

165

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Nov 28, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.080

.;T;T;.

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.67

T;.;T;T

MetaRNN

Benign

0.0032

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.64

.;N;N;.

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.20

N;N;.;.

REVEL

Benign

0.016

Sift

Benign

0.15

T;T;.;.

Sift4G

Benign

0.40

T;T;.;.

Polyphen

0.0

.;B;B;.

Vest4

0.19

MVP

0.18

MPC

0.71

ClinPred

0.011

GERP RS

-0.48

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.047

gMVP

0.050

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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