10-32947377-T-C

Variant summary

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

The NM_002211.4(ITGB1):c.-1+10768A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 150,414 control chromosomes in the GnomAD database, including 17,870 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 0.46 (17870 hom., cov: 28)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB1	NM_002211.4	c.-1+10768A>G		intron_variant		ENST00000302278.8
ITGB1	NM_133376.3	c.-1+10382A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1	ENST00000302278.8	c.-1+10768A>G		intron_variant		1	NM_002211.4	P4

Frequencies

GnomAD3 genomes AF: 0.456 AC: 68479 AN: 150296 Hom.: 17863 Cov.: 28

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.469

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.455 AC: 68500 AN: 150414 Hom.: 17870 Cov.: 28 AF XY: 0.454 AC XY: 33262 AN XY: 73284

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.470

Alfa AF: 0.530 Hom.: 10731

Bravo AF: 0.444

Asia WGS AF: 0.343 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.36
Dann	Benign	0.40

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

LitVar

Other links and lift over

dbSNP: rs2488336; hg19: chr10-33236305;