rs2040009

Positions:

• chr10-32930567-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.154-523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 151,988 control chromosomes in the GnomAD database, including 872 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 0.095 (872 hom., cov: 33)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

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 (AMR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB1	NM_002211.4	c.154-523G>A		intron_variant		ENST00000302278.8
ITGB1	NM_033668.2	c.154-523G>A		intron_variant
ITGB1	NM_133376.3	c.154-523G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1	ENST00000302278.8	c.154-523G>A		intron_variant		1	NM_002211.4	P4

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14368 AN: 151870 Hom.: 866 Cov.: 33

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0940

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

GnomAD4 genome AF: 0.0946 AC: 14383 AN: 151988 Hom.: 872 Cov.: 33 AF XY: 0.0991 AC XY: 7358 AN XY: 74262

Gnomad4 AFR AF: 0.0498

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.0911

Gnomad4 FIN AF: 0.0950

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.0963

Alfa AF: 0.0904 Hom.: 89

Bravo AF: 0.102

Asia WGS AF: 0.146 AC: 508 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	1.5
DANN	Benign	0.84

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: rs2040009; hg19: chr10-33219495;