rs11591508

chr10-32995725-C-T

Variant summary

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

The NR_184020.1(ITGB1-DT):n.270+9968C>T variant causes a intron, non coding transcript 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 NR_184020.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ITGB1-DT	NR_184020.1	n.270+9968C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1-DT	ENST00000450890.5	n.287+9968C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.0910

Gnomad4 NFE AF: 0.0636

Gnomad4 OTH AF: 0.0887

Alfa AF: 0.0722 Hom.: 604

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11591508; hg19: chr10-33284653;