NM_000212.3:c.1914-267G>T

Variant names:

• chr17-47300211-G-T
• rs12603582
• NM_000212.3:c.1914-267G>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000212.3(ITGB3):​c.1914-267G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,230 control chromosomes in the GnomAD database, including 2,979 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2979 hom., cov: 32)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.209
• Publications: 14 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 17-47300211-G-T is Benign according to our data. Variant chr17-47300211-G-T is described in ClinVar as [Benign]. Clinvar id is 1267923.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB3	NM_000212.3	c.1914-267G>T		intron_variant	Intron 11 of 14	ENST00000559488.7	NP_000203.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7	c.1914-267G>T		intron_variant	Intron 11 of 14	1	NM_000212.3	ENSP00000452786.2
ENSG00000259753	ENST00000560629.1	n.1878-267G>T		intron_variant	Intron 11 of 17	2		ENSP00000456711.2

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27711 AN: 152114 Hom.: 2980 Cov.: 32

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.182 AC: 27719 AN: 152230 Hom.: 2979 Cov.: 32 AF XY: 0.184 AC XY: 13705 AN XY: 74428

African (AFR) AF: 0.0783 AC: 3253 AN: 41548

American (AMR) AF: 0.176 AC: 2699 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1132 AN: 5180

South Asian (SAS) AF: 0.174 AC: 840 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2914 AN: 10596

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15451 AN: 68000

Other (OTH) AF: 0.188 AC: 397 AN: 2110

Alfa AF: 0.204 Hom.: 7044

Bravo AF: 0.174

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.9
DANN	Benign	0.77
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.16		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: rs12603582; hg19: chr17-45377577;