10-32954879-G-C

Variant names:

• chr10-32954879-G-C
• rs1187072
• NM_002211.4:c.-1+3266C>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.-1+3266C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,030 control chromosomes in the GnomAD database, including 10,710 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 0.33 (10710 hom., cov: 32)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 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.-1+3266C>G		intron	N/A	NP_002202.2
	ITGB1	NM_133376.3		c.-1+2880C>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.-1+3266C>G		intron	N/A	ENSP00000303351.3
	ITGB1	ENST00000488427.2	TSL:1	c.-162+3266C>G		intron	N/A	ENSP00000417508.2
	ITGB1	ENST00000677310.2		c.-217-1070C>G		intron	N/A	ENSP00000504508.1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50625 AN: 151912 Hom.: 10709 Cov.: 32

Gnomad AFR AF: 0.0898

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0972

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.333 AC: 50625 AN: 152030 Hom.: 10710 Cov.: 32 AF XY: 0.329 AC XY: 24435 AN XY: 74314

African (AFR) AF: 0.0896 AC: 3714 AN: 41452

American (AMR) AF: 0.335 AC: 5120 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1582 AN: 3464

East Asian (EAS) AF: 0.0974 AC: 503 AN: 5162

South Asian (SAS) AF: 0.275 AC: 1321 AN: 4812

European-Finnish (FIN) AF: 0.451 AC: 4761 AN: 10562

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32441 AN: 67992

Other (OTH) AF: 0.348 AC: 731 AN: 2100

Alfa AF: 0.296 Hom.: 925

Bravo AF: 0.314

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		0.27
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: rs1187072; hg19: chr10-33243807;