rs11009157

Positions:

• chr10-32953473-G-A
• chr10-32953473-G-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+4672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,844 control chromosomes in the GnomAD database, including 5,123 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 0.26 (5122 hom., cov: 31)
  • Exomes 𝑓: 0.40 (1 hom.)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

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 (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB1	NM_002211.4	c.-1+4672C>T		intron_variant		ENST00000302278.8
ITGB1	NM_133376.3	c.-1+4286C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1	ENST00000302278.8	c.-1+4672C>T		intron_variant		1	NM_002211.4	P4

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38798 AN: 151704 Hom.: 5122 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.281

GnomAD4 exome AF: 0.400 AC: 8 AN: 20 Hom.: 1 AF XY: 0.375 AC XY: 6 AN XY: 16

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.256 AC: 38813 AN: 151824 Hom.: 5122 Cov.: 31 AF XY: 0.259 AC XY: 19175 AN XY: 74176

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.283

Alfa AF: 0.253 Hom.: 7006

Bravo AF: 0.254

Asia WGS AF: 0.443 AC: 1539 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	4.3
DANN	Benign	0.37

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: rs11009157; hg19: chr10-33242401;