rs3809863

chr17-47307646-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000212.3(ITGB3):c.2301+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 1,612,228 control chromosomes in the GnomAD database, including 174,909 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.46 (16187 hom., cov: 32)
  • Exomes 𝑓: 0.46 (158722 hom.)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Benign reviewed by expert panel B:5
• Conservation: PhyloP100: 0.370

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]

EFCAB13-DT (HGNC:55338): (EFCAB13 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 17-47307646-C-T is Benign according to our data. Variant chr17-47307646-C-T is described in ClinVar as [Benign]. Clinvar id is 255539.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-47307646-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB3	NM_000212.3	c.2301+9C>T		intron_variant		ENST00000559488.7
EFCAB13-DT	NR_110880.1	n.363-3864G>A		intron_variant, non_coding_transcript_variant
EFCAB13-DT	NR_110881.1	n.227-3864G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB3	ENST00000559488.7	c.2301+9C>T		intron_variant		1	NM_000212.3	P1
EFCAB13-DT	ENST00000575039.1	n.227-3864G>A		intron_variant, non_coding_transcript_variant		5
ITGB3	ENST00000696963.1	c.2310C>T	p.Asp770=	synonymous_variant	14/14

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69311 AN: 151934 Hom.: 16185 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.439

GnomAD3 exomes AF: 0.429 AC: 107220 AN: 249968 Hom.: 23739 AF XY: 0.431 AC XY: 58200 AN XY: 135070

Gnomad AFR exome AF: 0.482

Gnomad AMR exome AF: 0.354

Gnomad ASJ exome AF: 0.419

Gnomad EAS exome AF: 0.249

Gnomad SAS exome AF: 0.390

Gnomad FIN exome AF: 0.494

Gnomad NFE exome AF: 0.472

Gnomad OTH exome AF: 0.432

GnomAD4 exome AF: 0.463 AC: 676003 AN: 1460176 Hom.: 158722 Cov.: 36 AF XY: 0.461 AC XY: 335190 AN XY: 726390

Gnomad4 AFR exome AF: 0.475

Gnomad4 AMR exome AF: 0.356

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.269

Gnomad4 SAS exome AF: 0.389

Gnomad4 FIN exome AF: 0.493

Gnomad4 NFE exome AF: 0.480

Gnomad4 OTH exome AF: 0.453

GnomAD4 genome AF: 0.456 AC: 69347 AN: 152052 Hom.: 16187 Cov.: 32 AF XY: 0.453 AC XY: 33674 AN XY: 74310

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.438

Alfa AF: 0.463 Hom.: 38935

Bravo AF: 0.449

Asia WGS AF: 0.295 AC: 1027 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: reviewed by expert panel

Submissions by phenotype

Glanzmann thrombasthenia Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, reviewed by expert panel	curation	ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen	Apr 06, 2023	After a comprehensive literature search of the intronic variant NM_000212.3(ITGB3):c.2301+9C>T, no individuals with Glanzmann Thrombasthenia were reported with the variant. The variant has a high minor allele frequency of 0.4805 (11916/24800 alleles) in the African/African American population, which is higher than the ClinGen PD VCEP threshold (>0.0024), and therefore meets BA1. In silico predictor spliceAI revealed that the intronic mutation is not expected to impact splicing and a PhyloP score of -.336 shows that the nucleotide position is not highly conserved (BP4,BP7). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: BA1, BP4 and BP7 (PD VCEP specifications version 2.1). -

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 08, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	11
Dann	Benign	0.87

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: rs3809863; hg19: chr17-45385012;