10-32971771-G-A

Variant names:

• chr10-32971771-G-A
• rs17296289
• ENST00000534049.5:c.-1+20560C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

ITGB1-DT (HGNC:53718): (ITGB1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000534049.5	c.-1+20560C>T		intron_variant	Intron 1 of 4	4		ENSP00000431326.1
ITGB1-DT	ENST00000450890.6	n.485+10709G>A		intron_variant	Intron 2 of 3	3
ITGB1	ENST00000475184.6	n.178+33844C>T		intron_variant	Intron 1 of 6	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

African (AFR) AF: 0.0127 AC: 530 AN: 41570

American (AMR) AF: 0.0702 AC: 1073 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.187 AC: 970 AN: 5188

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4812

European-Finnish (FIN) AF: 0.0887 AC: 940 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0646 AC: 4393 AN: 67992

Other (OTH) AF: 0.0690 AC: 146 AN: 2116

Alfa AF: 0.0644 Hom.: 609

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs17296289; hg19: chr10-33260699;