10-32908460-A-C

Variant names:

• chr10-32908460-A-C
• NM_002211.4:c.2239T>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_002211.4(ITGB1):​c.2239T>G​(p.Leu747Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ITGB1 NM_002211.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.85
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1	NM_002211.4	c.2239T>G	p.Leu747Val	missense_variant	Exon 15 of 16	ENST00000302278.8	NP_002202.2
ITGB1	NM_033668.2	c.2239T>G	p.Leu747Val	missense_variant	Exon 14 of 16		NP_391988.1
ITGB1	NM_133376.3	c.2239T>G	p.Leu747Val	missense_variant	Exon 15 of 16		NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.2239T>G	p.Leu747Val	missense_variant	Exon 15 of 16	1	NM_002211.4	ENSP00000303351.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 26, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2239T>G (p.L747V) alteration is located in exon 14 (coding exon 14) of the ITGB1 gene. This alteration results from a T to G substitution at nucleotide position 2239, causing the leucine (L) at amino acid position 747 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.45
BayesDel_addAF	Pathogenic	0.23	D
BayesDel_noAF	Uncertain	0.090
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.57	.;D;D
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.35
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.94	D;D;.
M_CAP	Pathogenic	0.30	D
MetaRNN	Uncertain	0.62	D;D;D
MetaSVM	Uncertain	0.67	D
MutationAssessor	Uncertain	2.6	M;M;M
PhyloP100		1.9
PrimateAI	Pathogenic	0.87	D
PROVEAN	Benign	-1.5	N;N;N
REVEL	Pathogenic	0.65
Sift	Uncertain	0.019	D;D;D
Sift4G	Benign	0.098	T;T;T
Polyphen		1.0	D;D;D
Vest4		0.58
MutPred		0.41		Gain of methylation at K752 (P = 0.0803);Gain of methylation at K752 (P = 0.0803);Gain of methylation at K752 (P = 0.0803);
MVP		0.90
MPC		1.9
ClinPred		0.87	D
GERP RS		2.2
Varity_R		0.17
gMVP		0.90
Mutation Taster		=87/13	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

hg19: chr10-33197388;