X-70149003-T-C

Position:

• chrX-70149003-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_001551.3(IGBP1):​c.758+163T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.84 (27590 hom., 28095 hem., cov: 23)
  • Exomes 𝑓: 0.87 (93174 hom. 103308 hem.)
  • Failed GnomAD Quality Control
• Consequence: IGBP1 NM_001551.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.52

Genes affected

IGBP1 (HGNC:5461): (immunoglobulin binding protein 1) The proliferation and differentiation of B cells is dependent upon a B-cell antigen receptor (BCR) complex. Binding of antigens to specific B-cell receptors results in a tyrosine phosphorylation reaction through the BCR complex and leads to multiple signal transduction pathways. [provided by RefSeq, Jul 2008]

IGBP1-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP6: Variant X-70149003-T-C is Benign according to our data. Variant chrX-70149003-T-C is described in ClinVar as [Benign]. Clinvar id is 1257271.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGBP1	NM_001551.3	c.758+163T>C		intron_variant		ENST00000356413.5	NP_001542.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGBP1	ENST00000356413.5	c.758+163T>C		intron_variant		1	NM_001551.3	ENSP00000348784.4
IGBP1	ENST00000342206.10	c.758+163T>C		intron_variant		1		ENSP00000363661.5
IGBP1-AS2	ENST00000403371.2	n.127-35A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.842 AC: 93302 AN: 110832 Hom.: 27592 Cov.: 23 AF XY: 0.846 AC XY: 28040 AN XY: 33148

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.871

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.866 AC: 316751 AN: 365782 Hom.: 93174 Cov.: 4 AF XY: 0.859 AC XY: 103308 AN XY: 120268

Gnomad4 AFR exome AF: 0.760

Gnomad4 AMR exome AF: 0.944

Gnomad4 ASJ exome AF: 0.915

Gnomad4 EAS exome AF: 0.970

Gnomad4 SAS exome AF: 0.731

Gnomad4 FIN exome AF: 0.902

Gnomad4 NFE exome AF: 0.865

Gnomad4 OTH exome AF: 0.872

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.842 AC: 93349 AN: 110885 Hom.: 27590 Cov.: 23 AF XY: 0.846 AC XY: 28095 AN XY: 33213

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.873

Alfa AF: 0.857 Hom.: 7401

Bravo AF: 0.843

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.13

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: rs650028; hg19: chrX-69368853;