chr10-32908269-A-C

Variant names:

• chr10-32908269-A-C
• rs1316757
• NM_002211.4:c.2331+99T>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.2331+99T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,154,740 control chromosomes in the GnomAD database, including 8,218 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 0.090 (890 hom., cov: 32)
  • Exomes 𝑓: 0.11 (7328 hom.)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 16 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 (EAS) allele frequency at 95% confidence interval = 0.314 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1	NM_002211.4	MANE Select	c.2331+99T>G		intron	N/A	NP_002202.2
	ITGB1	NM_033668.2		c.2331+99T>G		intron	N/A	NP_391988.1	P05556-5
	ITGB1	NM_133376.3		c.2331+99T>G		intron	N/A	NP_596867.1	P05556-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1	ENST00000302278.8	TSL:1 MANE Select	c.2331+99T>G		intron	N/A	ENSP00000303351.3	P05556-1
	ITGB1	ENST00000488427.2	TSL:1	c.2160+99T>G		intron	N/A	ENSP00000417508.2	H7C4K3
	ITGB1	ENST00000676460.1		c.*60T>G		3_prime_UTR	Exon 15 of 15	ENSP00000504641.1	P05556-2

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13787 AN: 152144 Hom.: 896 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0948

GnomAD4 exome AF: 0.111 AC: 111472 AN: 1002478 Hom.: 7328 AF XY: 0.113 AC XY: 57980 AN XY: 515362

African (AFR) AF: 0.0274 AC: 656 AN: 23916

American (AMR) AF: 0.0794 AC: 3162 AN: 39828

Ashkenazi Jewish (ASJ) AF: 0.0933 AC: 2078 AN: 22282

East Asian (EAS) AF: 0.310 AC: 11597 AN: 37372

South Asian (SAS) AF: 0.129 AC: 9300 AN: 72364

European-Finnish (FIN) AF: 0.125 AC: 6538 AN: 52178

Middle Eastern (MID) AF: 0.123 AC: 579 AN: 4718

European-Non Finnish (NFE) AF: 0.103 AC: 72756 AN: 704998

Other (OTH) AF: 0.107 AC: 4806 AN: 44822

GnomAD4 genome AF: 0.0904 AC: 13765 AN: 152262 Hom.: 890 Cov.: 32 AF XY: 0.0931 AC XY: 6934 AN XY: 74472

African (AFR) AF: 0.0309 AC: 1283 AN: 41572

American (AMR) AF: 0.0870 AC: 1331 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 314 AN: 3472

East Asian (EAS) AF: 0.327 AC: 1693 AN: 5180

South Asian (SAS) AF: 0.134 AC: 646 AN: 4822

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10600

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6937 AN: 68010

Other (OTH) AF: 0.0934 AC: 197 AN: 2110

Alfa AF: 0.0954 Hom.: 982

Bravo AF: 0.0850

Asia WGS AF: 0.166 AC: 577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		0.098
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: rs1316757; hg19: chr10-33197197; COSMIC: COSV56480845;