10-32953473-G-A

Variant names:

• chr10-32953473-G-A
• rs11009157
• NM_002211.4:c.-1+4672C>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+4672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,844 control chromosomes in the GnomAD database, including 5,123 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 0.26 (5122 hom., cov: 31)
  • Exomes 𝑓: 0.40 (1 hom.)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 23 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 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+4672C>T		intron	N/A	NP_002202.2
	ITGB1	NM_133376.3		c.-1+4286C>T		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+4672C>T		intron	N/A	ENSP00000303351.3
	ITGB1	ENST00000488427.2	TSL:1	c.-162+4672C>T		intron	N/A	ENSP00000417508.2
	ITGB1	ENST00000677310.2		c.-1+120C>T		intron	N/A	ENSP00000504508.1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38798 AN: 151704 Hom.: 5122 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.281

GnomAD4 exome AF: 0.400 AC: 8 AN: 20 Hom.: 1 AF XY: 0.375 AC XY: 6 AN XY: 16

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) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 6 AN: 16

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.256 AC: 38813 AN: 151824 Hom.: 5122 Cov.: 31 AF XY: 0.259 AC XY: 19175 AN XY: 74176

African (AFR) AF: 0.224 AC: 9288 AN: 41390

American (AMR) AF: 0.255 AC: 3897 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3466

East Asian (EAS) AF: 0.413 AC: 2120 AN: 5134

South Asian (SAS) AF: 0.450 AC: 2165 AN: 4814

European-Finnish (FIN) AF: 0.227 AC: 2380 AN: 10488

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16999 AN: 67952

Other (OTH) AF: 0.283 AC: 599 AN: 2114

Alfa AF: 0.253 Hom.: 15290

Bravo AF: 0.254

Asia WGS AF: 0.443 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.37
PhyloP100		-0.090
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: rs11009157; hg19: chr10-33242401;