rs650028

Variant names:

• chrX-70149003-T-A
• rs650028
• NM_001551.3:c.758+163T>A

Your query was ambiguous. Multiple possible variants found:

• chrX-70149003-T-A
• chrX-70149003-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001551.3(IGBP1):​c.758+163T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: IGBP1 NM_001551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 1 publications found

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:40294): (IGBP1 antisense RNA 2)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGBP1	NM_001551.3	MANE Select	c.758+163T>A		intron	N/A	NP_001542.1	P78318
	IGBP1	NM_001370192.1		c.758+163T>A		intron	N/A	NP_001357121.1	P78318
	IGBP1	NM_001370193.1		c.758+163T>A		intron	N/A	NP_001357122.1	P78318

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGBP1	ENST00000356413.5	TSL:1 MANE Select	c.758+163T>A		intron	N/A	ENSP00000348784.4	P78318
	IGBP1	ENST00000342206.10	TSL:1	c.758+163T>A		intron	N/A	ENSP00000363661.5	P78318
	IGBP1	ENST00000937166.1		c.758+163T>A		intron	N/A	ENSP00000607225.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 366008 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 120320

African (AFR) AF: 0.00 AC: 0 AN: 11525

American (AMR) AF: 0.00 AC: 0 AN: 25040

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12368

East Asian (EAS) AF: 0.00 AC: 0 AN: 21746

South Asian (SAS) AF: 0.00 AC: 0 AN: 33927

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25839

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2727

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 211989

Other (OTH) AF: 0.00 AC: 0 AN: 20847

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.34
PhyloP100		-2.5

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

Other links and lift over

dbSNP: rs650028; hg19: chrX-69368853;