Genetic Variant NM_001551.3:c.758+163T>C (chrX-70149003-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBP6_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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.52

Publications

1 publications found

Variant links:

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 links:

IGBP1-AS2 (HGNC:40294): (IGBP1 antisense RNA 2)

IGBP1-AS2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 1257271.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.842

AC:

93302

AN:

110832

Hom.:

27592

Cov.:

show subpopulations

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.:

AF XY:

0.859

AC XY:

103308

AN XY:

120268

show subpopulations

African (AFR)

AF:

0.760

AC:

8758

AN:

11517

American (AMR)

AF:

0.944

AC:

23633

AN:

25035

Ashkenazi Jewish (ASJ)

AF:

0.915

AC:

11312

AN:

12359

East Asian (EAS)

AF:

0.970

AC:

21087

AN:

21744

South Asian (SAS)

AF:

0.731

AC:

24776

AN:

33913

European-Finnish (FIN)

AF:

0.902

AC:

23290

AN:

25816

Middle Eastern (MID)

AF:

0.888

AC:

2420

AN:

2725

European-Non Finnish (NFE)

AF:

0.865

AC:

183311

AN:

211843

Other (OTH)

AF:

0.872

AC:

18164

AN:

20830

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1394

2789

4183

5578

6972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1002

2004

3006

4008

5010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.842

AC:

93349

AN:

110885

Hom.:

27590

Cov.:

AF XY:

0.846

AC XY:

28095

AN XY:

33213

show subpopulations

African (AFR)

AF:

0.761

AC:

23203

AN:

30505

American (AMR)

AF:

0.910

AC:

9580

AN:

10525

Ashkenazi Jewish (ASJ)

AF:

0.913

AC:

2416

AN:

2646

East Asian (EAS)

AF:

0.943

AC:

3267

AN:

3466

South Asian (SAS)

AF:

0.721

AC:

1940

AN:

2689

European-Finnish (FIN)

AF:

0.903

AC:

5259

AN:

5823

Middle Eastern (MID)

AF:

0.883

AC:

188

AN:

213

European-Non Finnish (NFE)

AF:

0.862

AC:

45511

AN:

52825

Other (OTH)

AF:

0.873

AC:

1318

AN:

1510

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

528

1056

1584

2112

2640

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

770

1540

2310

3080

3850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.857

Hom.:

7401

Bravo

AF:

0.843

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.30

(source)

DANN

Benign

0.13

PhyloP100

-2.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over