NM_002211.4:c.-1+3266C>G

Variant names:

• chr10-32954879-G-C
• rs1187072
• NM_002211.4:c.-1+3266C>G

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1	NM_002211.4	c.-1+3266C>G		intron_variant	Intron 1 of 15	ENST00000302278.8	NP_002202.2
ITGB1	NM_133376.3	c.-1+2880C>G		intron_variant	Intron 1 of 15		NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.-1+3266C>G		intron_variant	Intron 1 of 15	1	NM_002211.4	ENSP00000303351.3

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

Gnomad4 AFR AF: 0.0896

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.0974

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.348

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.56

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: rs1187072; hg19: chr10-33243807;