rs7214096

Variant names:

• chr17-47293152-G-A
• rs7214096
• NM_000212.3:c.1690+584G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000212.3(ITGB3):​c.1690+584G>A 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 152,176 control chromosomes in the GnomAD database, including 1,386 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 (1386 hom., cov: 32)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 6 publications found

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:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt
ITGB3	NM_000212.3	c.1690+584G>A		intron_variant	Intron 10 of 14	ENST00000559488.7	NP_000203.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7	c.1690+584G>A		intron_variant	Intron 10 of 14	1	NM_000212.3	ENSP00000452786.2
ENSG00000259753	ENST00000560629.1	n.1654+584G>A		intron_variant	Intron 10 of 17	2		ENSP00000456711.2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19443 AN: 152060 Hom.: 1386 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.142

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: 19443 AN: 152176 Hom.: 1386 Cov.: 32 AF XY: 0.125 AC XY: 9316 AN XY: 74392

African (AFR) AF: 0.105 AC: 4370 AN: 41510

American (AMR) AF: 0.102 AC: 1554 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3470

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5186

South Asian (SAS) AF: 0.0989 AC: 476 AN: 4812

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10590

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10613 AN: 68004

Other (OTH) AF: 0.141 AC: 299 AN: 2116

Alfa AF: 0.147 Hom.: 2836

Bravo AF: 0.124

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.41
PhyloP100		0.21
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: rs7214096; hg19: chr17-45370518;