10-32930080-T-G

Position:

• chr10-32930080-T-G

Variant summary

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

The NM_002211.4(ITGB1):​c.154-36A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 828,366 control chromosomes in the GnomAD database, including 170,363 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 0.54 (24930 hom., cov: 32)
  • Exomes 𝑓: 0.65 (145433 hom.)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB1	NM_002211.4	c.154-36A>C		intron_variant		ENST00000302278.8	NP_002202.2
ITGB1	NM_033668.2	c.154-36A>C		intron_variant			NP_391988.1
ITGB1	NM_133376.3	c.154-36A>C		intron_variant			NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.154-36A>C		intron_variant		1	NM_002211.4	ENSP00000303351.3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81446 AN: 151882 Hom.: 24925 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.549

GnomAD3 exomes AF: 0.628 AC: 137899 AN: 219666 Hom.: 45026 AF XY: 0.636 AC XY: 76249 AN XY: 119806

Gnomad AFR exome AF: 0.220

Gnomad AMR exome AF: 0.683

Gnomad ASJ exome AF: 0.676

Gnomad EAS exome AF: 0.433

Gnomad SAS exome AF: 0.676

Gnomad FIN exome AF: 0.668

Gnomad NFE exome AF: 0.678

Gnomad OTH exome AF: 0.633

GnomAD4 exome AF: 0.649 AC: 438631 AN: 676366 Hom.: 145433 Cov.: 6 AF XY: 0.652 AC XY: 236000 AN XY: 361962

Gnomad4 AFR exome AF: 0.222

Gnomad4 AMR exome AF: 0.669

Gnomad4 ASJ exome AF: 0.674

Gnomad4 EAS exome AF: 0.441

Gnomad4 SAS exome AF: 0.672

Gnomad4 FIN exome AF: 0.661

Gnomad4 NFE exome AF: 0.679

Gnomad4 OTH exome AF: 0.617

GnomAD4 genome AF: 0.536 AC: 81466 AN: 152000 Hom.: 24930 Cov.: 32 AF XY: 0.539 AC XY: 40032 AN XY: 74272

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.552

Alfa AF: 0.608 Hom.: 5562

Bravo AF: 0.519

Asia WGS AF: 0.569 AC: 1978 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2256455; hg19: chr10-33219008; COSMIC: COSV56488043; COSMIC: COSV56488043;