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

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.125

Gnomad4 SAS exome

AF:

0.241

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.506

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.328

AC:

49611

AN:

151348

Hom.:

10337

Cov.:

AF XY:

0.324

AC XY:

23926

AN XY:

73912

show subpopulations

Gnomad4 AFR

AF:

0.0904

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.462

Gnomad4 EAS

AF:

0.0775

Gnomad4 SAS

AF:

0.284

Gnomad4 FIN

AF:

0.455

Gnomad4 NFE

AF:

0.472

Gnomad4 OTH

AF:

0.342

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

DANN

Benign

0.95

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over