rs1187075

Variant names:

• chr10-32957868-A-G
• rs1187075
• NM_002211.4:c.-1+277T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-32957868-A-G
• chr10-32957868-A-T

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+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
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 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+277T>C		intron	N/A	NP_002202.2
	ITGB1	NM_133376.3		c.-110T>C		5_prime_UTR	Exon 1 of 16	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+277T>C		intron	N/A	ENSP00000303351.3
	ITGB1	ENST00000488427.2	TSL:1	c.-162+277T>C		intron	N/A	ENSP00000417508.2
	ITGB1	ENST00000396033.6	TSL:5	c.-110T>C		5_prime_UTR	Exon 1 of 16	ENSP00000379350.2

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

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.887 AC: 71 AN: 80

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.697 AC: 28891 AN: 41462

American (AMR) AF: 0.879 AC: 13438 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3152 AN: 3468

East Asian (EAS) AF: 0.686 AC: 3501 AN: 5104

South Asian (SAS) AF: 0.868 AC: 4185 AN: 4822

European-Finnish (FIN) AF: 0.879 AC: 9274 AN: 10550

Middle Eastern (MID) AF: 0.869 AC: 252 AN: 290

European-Non Finnish (NFE) AF: 0.896 AC: 60867 AN: 67902

Other (OTH) AF: 0.855 AC: 1800 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.1
DANN	Benign	0.28
PhyloP100		-4.3
PromoterAI		0.0010	Neutral
Mutation Taster		=300/0	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: rs1187075; hg19: chr10-33246796;