rs1187076

chr10-32957952-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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]

ACMG classification

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/exons	MANE	UniProt
ITGB1	NM_002211.4	c.-1+193G>A		intron_variant		ENST00000302278.8
ITGB1	NM_133376.3	c.-194G>A		5_prime_UTR_variant	1/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1	ENST00000302278.8	c.-1+193G>A		intron_variant		1	NM_002211.4	P4

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49609 AN: 151242 Hom.: 10336 Cov.: 31

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.: 35 Cov.: 0 AF XY: 0.392 AC XY: 98 AN XY: 250

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.: 31 AF XY: 0.324 AC XY: 23926 AN XY: 73912

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	14
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1187076; hg19: chr10-33246880;