X-70149119-T-G

Position:

• chrX-70149119-T-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001551.3(IGBP1):​c.758+279T>G 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 (27057 hom., 26764 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: IGBP1 NM_001551.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.214

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant X-70149119-T-G is Benign according to our data. Variant chrX-70149119-T-G is described in ClinVar as [Benign]. Clinvar id is 1262781.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGBP1	NM_001551.3	c.758+279T>G		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+279T>G		intron_variant		1	NM_001551.3	ENSP00000348784.4
IGBP1	ENST00000342206.10	c.758+279T>G		intron_variant		1		ENSP00000363661.5
IGBP1-AS2	ENST00000403371.2	n.127-151A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.836 AC: 91327 AN: 109260 Hom.: 27058 Cov.: 22 AF XY: 0.846 AC XY: 26721 AN XY: 31590

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.865

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.836 AC: 91364 AN: 109303 Hom.: 27057 Cov.: 22 AF XY: 0.846 AC XY: 26764 AN XY: 31643

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.867

Alfa AF: 0.744 Hom.: 2730

Bravo AF: 0.834

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

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.51

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: rs649554; hg19: chrX-69368969;