rs369919013

Variant summary

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

The NM_001256447.2(BCAP31):​c.702+13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,205,323 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 37 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00040 ( 0 hom., 6 hem., cov: 25)
Exomes 𝑓: 0.000084 ( 0 hom. 31 hem. )

Consequence

BCAP31
NM_001256447.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.434
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]

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 (BayesDel_noAF=-0.87).
BP6
Variant X-153701994-C-T is Benign according to our data. Variant chrX-153701994-C-T is described in ClinVar as [Benign]. Clinvar id is 1899325.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAd4 at 6 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BCAP31NM_001256447.2 linkc.702+13G>A intron_variant Intron 7 of 7 ENST00000345046.12 NP_001243376.1 P51572-1
BCAP31NM_001139457.2 linkc.903+13G>A intron_variant Intron 7 of 7 NP_001132929.1 P51572-2
BCAP31NM_001139441.1 linkc.702+13G>A intron_variant Intron 7 of 7 NP_001132913.1 P51572-1
BCAP31NM_005745.8 linkc.702+13G>A intron_variant Intron 7 of 7 NP_005736.3 P51572-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BCAP31ENST00000345046.12 linkc.702+13G>A intron_variant Intron 7 of 7 1 NM_001256447.2 ENSP00000343458.6 P51572-1

Frequencies

GnomAD3 genomes
AF:
0.000398
AC:
45
AN:
112997
Hom.:
0
Cov.:
25
AF XY:
0.000171
AC XY:
6
AN XY:
35127
show subpopulations
Gnomad AFR
AF:
0.00119
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000279
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:
0.0000937
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000102
AC:
18
AN:
177056
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
62074
show subpopulations
Gnomad AFR exome
AF:
0.00101
Gnomad AMR exome
AF:
0.0000749
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:
0.0000380
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000842
AC:
92
AN:
1092326
Hom.:
0
Cov.:
28
AF XY:
0.0000865
AC XY:
31
AN XY:
358362
show subpopulations
Gnomad4 AFR exome
AF:
0.000724
Gnomad4 AMR exome
AF:
0.000114
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:
0.0000764
Gnomad4 OTH exome
AF:
0.0000872
GnomAD4 genome
AF:
0.000398
AC:
45
AN:
112997
Hom.:
0
Cov.:
25
AF XY:
0.000171
AC XY:
6
AN XY:
35127
show subpopulations
Gnomad4 AFR
AF:
0.00119
Gnomad4 AMR
AF:
0.000279
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000937
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000214
Hom.:
0
Bravo
AF:
0.000442

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 02, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.64
DANN
Benign
0.43
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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.

Other links and lift over

dbSNP: rs369919013; hg19: chrX-152967449; API