rs17296289

Positions:

• chr10-32971771-G-A
• chr10-32971771-G-C

Variant summary

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

The ENST00000534049.5(ITGB1):​c.-1+20560C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 152,238 control chromosomes in the GnomAD database, including 504 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 0.062 (504 hom., cov: 32)
• Consequence: ITGB1 ENST00000534049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32971771G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000534049.5	c.-1+20560C>T		intron_variant		4		ENSP00000431326.1
ITGB1-DT	ENST00000450890.5	n.152+10709G>A		intron_variant		3
ITGB1	ENST00000475184.6	n.178+33844C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0623 AC: 9482 AN: 152120 Hom.: 503 Cov.: 32

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0623 AC: 9481 AN: 152238 Hom.: 504 Cov.: 32 AF XY: 0.0679 AC XY: 5056 AN XY: 74426

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.0887

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0664 Hom.: 500

Bravo AF: 0.0562

Asia WGS AF: 0.220 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17296289; hg19: chr10-33260699;