rs1187075

chr10-32957868-A-Gchr10-32957868-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002211.4(ITGB1):c.-1+277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 151,990 control chromosomes in the GnomAD database, including 53,166 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 0.83 (53130 hom., cov: 33)
  • Exomes 𝑓: 0.88 (36 hom.)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.26

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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB1	NM_002211.4	c.-1+277T>C		intron_variant		ENST00000302278.8
ITGB1	NM_133376.3	c.-110T>C		5_prime_UTR_variant	1/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1	ENST00000302278.8	c.-1+277T>C		intron_variant		1	NM_002211.4	P4

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126149 AN: 151788 Hom.: 53094 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.875

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.853

GnomAD4 exome AF: 0.880 AC: 81 AN: 92 Hom.: 36 Cov.: 0 AF XY: 0.897 AC XY: 61 AN XY: 68

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.887

GnomAD4 genome AF: 0.831 AC: 126234 AN: 151898 Hom.: 53130 Cov.: 33 AF XY: 0.831 AC XY: 61675 AN XY: 74252

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.855

Alfa AF: 0.868 Hom.: 6760

Bravo AF: 0.824

Asia WGS AF: 0.824 AC: 2835 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	3.1
Dann	Benign	0.28

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: rs1187075; hg19: chr10-33246796;