10-32889379-T-C

Variant names:

• chr10-32889379-T-C
• rs1557150
• ENST00000609742.3:c.2332-377A>G

Variant summary

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

The ENST00000609742.3(ITGB1):​c.2332-377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,124 control chromosomes in the GnomAD database, including 5,236 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 0.24 (5236 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ITGB1 ENST00000609742.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000609742.3	c.2332-377A>G		intron_variant	Intron 15 of 15	6		ENSP00000503306.1
ITGB1	ENST00000678989.1	n.*59-377A>G		intron_variant	Intron 16 of 16			ENSP00000502882.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35878 AN: 152006 Hom.: 5244 Cov.: 33

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.236 AC: 35862 AN: 152124 Hom.: 5236 Cov.: 33 AF XY: 0.238 AC XY: 17719 AN XY: 74360

Gnomad4 AFR AF: 0.0814

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.274

Alfa AF: 0.270 Hom.: 2600

Bravo AF: 0.229

Asia WGS AF: 0.371 AC: 1277 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557150; hg19: chr10-33178307;