10-32925037-G-C

Variant names:

• chr10-32925037-G-C
• rs3780871
• NM_002211.4:c.786+834C>G

Variant summary

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

The NM_002211.4(ITGB1):​c.786+834C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,014 control chromosomes in the GnomAD database, including 1,703 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 0.14 (1703 hom., cov: 32)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002211.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1	NM_002211.4	MANE Select	c.786+834C>G		intron	N/A	NP_002202.2
	ITGB1	NM_033668.2		c.786+834C>G		intron	N/A	NP_391988.1
	ITGB1	NM_133376.3		c.786+834C>G		intron	N/A	NP_596867.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1	ENST00000302278.8	TSL:1 MANE Select	c.786+834C>G		intron	N/A	ENSP00000303351.3
	ITGB1	ENST00000488427.2	TSL:1	c.615+834C>G		intron	N/A	ENSP00000417508.2
	ITGB1	ENST00000677310.2		c.786+834C>G		intron	N/A	ENSP00000504508.1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20674 AN: 151894 Hom.: 1705 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.136 AC: 20680 AN: 152014 Hom.: 1703 Cov.: 32 AF XY: 0.137 AC XY: 10174 AN XY: 74306

African (AFR) AF: 0.0453 AC: 1878 AN: 41450

American (AMR) AF: 0.179 AC: 2742 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1275 AN: 5160

South Asian (SAS) AF: 0.166 AC: 799 AN: 4808

European-Finnish (FIN) AF: 0.154 AC: 1623 AN: 10564

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11097 AN: 67974

Other (OTH) AF: 0.167 AC: 353 AN: 2108

Alfa AF: 0.151 Hom.: 228

Bravo AF: 0.134

Asia WGS AF: 0.205 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.79
PhyloP100		0.21
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: rs3780871; hg19: chr10-33213965;