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_133376.3(ITGB1):c.-194G>A variant causes a 5 prime UTR 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_133376.3 5_prime_UTR

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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133376.3. 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
	ITGB1	NM_002211.4	MANE Select	c.-1+193G>A		intron	N/A	NP_002202.2
	ITGB1	NM_133376.3		c.-194G>A		5_prime_UTR	Exon 1 of 16	NP_596867.1	P05556-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITGB1	ENST00000302278.8	TSL:1 MANE Select	c.-1+193G>A	intron	N/A	ENSP00000303351.3	P05556-1
ITGB1	ENST00000488427.2	TSL:1	c.-162+193G>A	intron	N/A	ENSP00000417508.2	H7C4K3
ITGB1	ENST00000898630.1		c.-715G>A	5_prime_UTR	Exon 1 of 16	ENSP00000568689.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over