chr10-32908395-C-CT

Position:

• chr10-32908395-C-CT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002211.4(ITGB1):​c.2303_2304insA​(p.Glu769GlyfsTer11) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as risk factor (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ITGB1 NM_002211.4 frameshift
• Clinical Significance: risk factor criteria provided, single submitter O:1
• Conservation: PhyloP100: 8.02

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB1	NM_002211.4	c.2303_2304insA	p.Glu769GlyfsTer11	frameshift_variant	15/16	ENST00000302278.8	NP_002202.2
ITGB1	NM_033668.2	c.2303_2304insA	p.Glu769GlyfsTer20	frameshift_variant	14/16		NP_391988.1
ITGB1	NM_133376.3	c.2303_2304insA	p.Glu769GlyfsTer11	frameshift_variant	15/16		NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.2303_2304insA	p.Glu769GlyfsTer11	frameshift_variant	15/16	1	NM_002211.4	ENSP00000303351	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

Neural tube defect Other:1

risk factor, criteria provided, single submitter

research

Laboratorio di Genetica e Neuroscienze, Istituto Giannina Gaslini

Jan 01, 2013

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Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs1565818580; hg19: chr10-33197323;