rs16941771

chr17-47262991-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.79+9051C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 152,246 control chromosomes in the GnomAD database, including 131 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 0.021 (131 hom., cov: 32)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB3	NM_000212.3	c.79+9051C>T		intron_variant		ENST00000559488.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB3	ENST00000559488.7	c.79+9051C>T		intron_variant		1	NM_000212.3	P1
ITGB3	ENST00000571680.1	c.79+9051C>T		intron_variant		1
ITGB3	ENST00000696963.1	c.79+9051C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3245 AN: 152128 Hom.: 130 Cov.: 32

Gnomad AFR AF: 0.00500

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0213 AC: 3250 AN: 152246 Hom.: 131 Cov.: 32 AF XY: 0.0240 AC XY: 1783 AN XY: 74446

Gnomad4 AFR AF: 0.00501

Gnomad4 AMR AF: 0.0215

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0149 Hom.: 5

Bravo AF: 0.0210

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.67
Dann	Benign	0.72

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: rs16941771; hg19: chr17-45340357;