X-153701109-GC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001256447.2(BCAP31):c.703-135del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 559,641 control chromosomes in the GnomAD database, including 847 homozygotes. There are 2,682 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.066 (596 hom., 1943 hem., cov: 20)
  • Exomes 𝑓: 0.0072 (251 hom. 739 hem.)
• Consequence: BCAP31 NM_001256447.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.599

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-153701109-GC-G is Benign according to our data. Variant chrX-153701109-GC-G is described in ClinVar as [Benign]. Clinvar id is 1267380.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAP31	NM_001256447.2	c.703-135del		intron_variant		ENST00000345046.12
BCAP31	NM_001139441.1	c.703-135del		intron_variant
BCAP31	NM_001139457.2	c.904-135del		intron_variant
BCAP31	NM_005745.8	c.703-135del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAP31	ENST00000345046.12	c.703-135del		intron_variant		1	NM_001256447.2	P1

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 7328 AN: 111278 Hom.: 595 Cov.: 20 AF XY: 0.0574 AC XY: 1926 AN XY: 33554

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0290

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00424

Gnomad NFE AF: 0.000680

Gnomad OTH AF: 0.0512

GnomAD4 exome AF: 0.00725 AC: 3250 AN: 448310 Hom.: 251 AF XY: 0.00596 AC XY: 739 AN XY: 124044

Gnomad4 AFR exome AF: 0.226

Gnomad4 AMR exome AF: 0.0170

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000964

Gnomad4 FIN exome AF: 0.0000276

Gnomad4 NFE exome AF: 0.000346

Gnomad4 OTH exome AF: 0.0202

GnomAD4 genome AF: 0.0660 AC: 7351 AN: 111331 Hom.: 596 Cov.: 20 AF XY: 0.0578 AC XY: 1943 AN XY: 33617

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000680

Gnomad4 OTH AF: 0.0505

Alfa AF: 0.0572 Hom.: 228

Bravo AF: 0.0783

Asia WGS AF: 0.0170 AC: 45 AN: 2522

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs202026017; hg19: chrX-152966564;