17-47264763-G-T

Variant summary

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

The NM_000212.3(ITGB3):c.80-9656G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,990 control chromosomes in the GnomAD database, including 5,575 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 (5575 hom., cov: 32)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

Genes affected

ITGB3 (HGNC:6156): (integrin subunit beta 3) The ITGB3 protein product is the integrin beta chain beta 3. Integrins are integral cell-surface proteins composed of an alpha chain and a beta chain. A given chain may combine with multiple partners resulting in different integrins. Integrin beta 3 is found along with the alpha IIb chain in platelets. Integrins are known to participate in cell adhesion as well as cell-surface mediated signalling. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB3	NM_000212.3	c.80-9656G>T		intron_variant		ENST00000559488.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB3	ENST00000559488.7	c.80-9656G>T		intron_variant		1	NM_000212.3	P1
ITGB3	ENST00000571680.1	c.80-9656G>T		intron_variant		1
ITGB3	ENST00000696963.1	c.80-9656G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40192 AN: 151872 Hom.: 5573 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.263

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.265 AC: 40217 AN: 151990 Hom.: 5575 Cov.: 32 AF XY: 0.262 AC XY: 19478 AN XY: 74282

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.260

Alfa AF: 0.245 Hom.: 9286

Bravo AF: 0.259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.42

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: rs10514919; hg19: chr17-45342129;