10-32889379-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609742.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1	ENST00000609742.3	TSL:6	c.2332-377A>G		intron	N/A	ENSP00000503306.1
	ITGB1	ENST00000678989.1		n.*59-377A>G		intron	N/A	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

African (AFR) AF: 0.0814 AC: 3381 AN: 41558

American (AMR) AF: 0.270 AC: 4127 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3466

East Asian (EAS) AF: 0.574 AC: 2967 AN: 5166

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4820

European-Finnish (FIN) AF: 0.289 AC: 3052 AN: 10558

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18957 AN: 67974

Other (OTH) AF: 0.274 AC: 577 AN: 2104

Alfa AF: 0.273 Hom.: 3625

Bravo AF: 0.229

Asia WGS AF: 0.371 AC: 1277 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1557150; hg19: chr10-33178307;