rs2040009

Variant names:

• chr10-32930567-C-T
• rs2040009
• NM_002211.4:c.154-523G>A

Variant summary

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

The NM_002211.4(ITGB1):​c.154-523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 151,988 control chromosomes in the GnomAD database, including 872 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 0.095 (872 hom., cov: 33)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1	NM_002211.4	c.154-523G>A		intron_variant	Intron 3 of 15	ENST00000302278.8	NP_002202.2
ITGB1	NM_033668.2	c.154-523G>A		intron_variant	Intron 2 of 15		NP_391988.1
ITGB1	NM_133376.3	c.154-523G>A		intron_variant	Intron 3 of 15		NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.154-523G>A		intron_variant	Intron 3 of 15	1	NM_002211.4	ENSP00000303351.3

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14368 AN: 151870 Hom.: 866 Cov.: 33

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0940

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

GnomAD4 genome AF: 0.0946 AC: 14383 AN: 151988 Hom.: 872 Cov.: 33 AF XY: 0.0991 AC XY: 7358 AN XY: 74262

African (AFR) AF: 0.0498 AC: 2065 AN: 41448

American (AMR) AF: 0.203 AC: 3105 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3472

East Asian (EAS) AF: 0.163 AC: 842 AN: 5170

South Asian (SAS) AF: 0.0911 AC: 439 AN: 4820

European-Finnish (FIN) AF: 0.0950 AC: 999 AN: 10516

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6138 AN: 67982

Other (OTH) AF: 0.0963 AC: 203 AN: 2108

Alfa AF: 0.0889 Hom.: 90

Bravo AF: 0.102

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.84
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2040009; hg19: chr10-33219495;