17-47275569-C-T

Position:

• chr17-47275569-C-T

Variant summary

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

The NM_000212.3(ITGB3):​c.165+1065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,194 control chromosomes in the GnomAD database, including 1,381 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 0.13 (1381 hom., cov: 32)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

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]

ENSG00000259753 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB3	NM_000212.3	c.165+1065C>T		intron_variant		ENST00000559488.7	NP_000203.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7	c.165+1065C>T		intron_variant		1	NM_000212.3	ENSP00000452786.2
ITGB3	ENST00000571680.1	c.165+1065C>T		intron_variant		1		ENSP00000461626.1
ENSG00000259753	ENST00000560629.1	n.129+1065C>T		intron_variant		2		ENSP00000456711.2
ITGB3	ENST00000696963.1	c.165+1065C>T		intron_variant				ENSP00000513002.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19468 AN: 152076 Hom.: 1381 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.128 AC: 19467 AN: 152194 Hom.: 1381 Cov.: 32 AF XY: 0.125 AC XY: 9322 AN XY: 74400

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.142

Alfa AF: 0.101 Hom.: 229

Bravo AF: 0.124

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.38
DANN	Benign	0.41

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: rs8069732; hg19: chr17-45352935;