dbSNP rs1187076: ITGB1:c.-1+193G>A (chr10-32957952-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002211.4(ITGB1):c.-1+193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,724 control chromosomes in the GnomAD database, including 10,372 homozygotes. 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: 𝑓 0.33 ( 10337 hom., cov: 31)

Exomes 𝑓: 0.37 ( 35 hom. )

Consequence

ITGB1
NM_002211.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980

Publications

3 publications found

Variant links:

Genes affected

ITGB1 (HGNC:6153): (integrin subunit beta 1) Integrins are heterodimeric proteins made up of alpha and beta subunits. At least 18 alpha and 8 beta subunits have been described in mammals. Integrin family members are membrane receptors involved in cell adhesion and recognition in a variety of processes including embryogenesis, hemostasis, tissue repair, immune response and metastatic diffusion of tumor cells. This gene encodes a beta subunit. Multiple alternatively spliced transcript variants which encode different protein isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ITGB1 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=-0.63).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1	NM_002211.4 link	c.-1+193G>A		intron_variant	Intron 1 of 15	ENST00000302278.8	NP_002202.2	P05556-1
ITGB1	NM_133376.3 link	c.-194G>A		5_prime_UTR_variant	Exon 1 of 16		NP_596867.1	P05556-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8 link	c.-1+193G>A		intron_variant	Intron 1 of 15	1	NM_002211.4	ENSP00000303351.3		P05556-1

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49609

AN:

151242

Hom.:

10336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0906

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.462

Gnomad EAS

AF:

0.0775

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.455

Gnomad MID

AF:

0.349

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.344

GnomAD4 exome

AF:

0.367

AC:

138

AN:

376

Hom.:

Cov.:

AF XY:

0.392

AC XY:

AN XY:

250

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.125

AC:

AN:

South Asian (SAS)

AF:

0.241

AC:

AN:

170

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.506

AC:

AN:

180

Other (OTH)

AF:

0.400

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.328

AC:

49611

AN:

151348

Hom.:

10337

Cov.:

AF XY:

0.324

AC XY:

23926

AN XY:

73912

show subpopulations

African (AFR)

AF:

0.0904

AC:

3742

AN:

41408

American (AMR)

AF:

0.309

AC:

4708

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.462

AC:

1599

AN:

3458

East Asian (EAS)

AF:

0.0775

AC:

396

AN:

5108

South Asian (SAS)

AF:

0.284

AC:

1370

AN:

4826

European-Finnish (FIN)

AF:

0.455

AC:

4729

AN:

10398

Middle Eastern (MID)

AF:

0.352

AC:

102

AN:

290

European-Non Finnish (NFE)

AF:

0.472

AC:

31924

AN:

67636

Other (OTH)

AF:

0.342

AC:

717

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1487

2975

4462

5950

7437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.402

Hom.:

1686

Bravo

AF:

0.306

Asia WGS

AF:

0.181

AC:

612

AN:

3386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.95

PhyloP100

-0.098

PromoterAI

-0.14

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over