rs11591508

Variant names:

• chr10-32995725-C-T
• rs11591508
• ENST00000414157.3:n.279+9963C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414157.3(ITGB1-DT):​n.279+9963C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,224 control chromosomes in the GnomAD database, including 909 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 0.096 (909 hom., cov: 32)
• Consequence: ITGB1-DT ENST00000414157.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 4 publications found

Genes affected

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

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1-DT	NR_184020.1	n.270+9968C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000414157.3	n.279+9963C>T		intron_variant	Intron 2 of 2	1
ITGB1-DT	ENST00000450890.6	n.620+9968C>T		intron_variant	Intron 3 of 3	3
ITGB1	ENST00000475184.6	n.178+9890G>A		intron_variant	Intron 1 of 6	4

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14621 AN: 152106 Hom.: 907 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0910

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0962 AC: 14638 AN: 152224 Hom.: 909 Cov.: 32 AF XY: 0.100 AC XY: 7478 AN XY: 74438

African (AFR) AF: 0.130 AC: 5384 AN: 41534

American (AMR) AF: 0.0768 AC: 1174 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1177 AN: 5178

South Asian (SAS) AF: 0.227 AC: 1091 AN: 4816

European-Finnish (FIN) AF: 0.0910 AC: 965 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0636 AC: 4327 AN: 68018

Other (OTH) AF: 0.0887 AC: 187 AN: 2108

Alfa AF: 0.0756 Hom.: 1619

Bravo AF: 0.0958

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs11591508; hg19: chr10-33284653;