17-47284929-C-T

Variant names:

• chr17-47284929-C-T
• rs2292699
• NM_000212.3:c.614+234C>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.614+234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,886 control chromosomes in the GnomAD database, including 12,230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.40 (12230 hom., cov: 32)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.850
• Publications: 9 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=-0.87).
• BP6: Variant 17-47284929-C-T is Benign according to our data. Variant chr17-47284929-C-T is described in ClinVar as Benign. ClinVar VariationId is 1242720.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB3	NM_000212.3	c.614+234C>T		intron_variant	Intron 4 of 14	ENST00000559488.7	NP_000203.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7	c.614+234C>T		intron_variant	Intron 4 of 14	1	NM_000212.3	ENSP00000452786.2
ENSG00000259753	ENST00000560629.1	n.578+234C>T		intron_variant	Intron 4 of 17	2		ENSP00000456711.2

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60074 AN: 151768 Hom.: 12207 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.396 AC: 60141 AN: 151886 Hom.: 12230 Cov.: 32 AF XY: 0.395 AC XY: 29339 AN XY: 74234

African (AFR) AF: 0.436 AC: 18030 AN: 41398

American (AMR) AF: 0.370 AC: 5649 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1486 AN: 3460

East Asian (EAS) AF: 0.575 AC: 2969 AN: 5164

South Asian (SAS) AF: 0.463 AC: 2221 AN: 4802

European-Finnish (FIN) AF: 0.320 AC: 3368 AN: 10540

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25032 AN: 67940

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.379 Hom.: 29817

Bravo AF: 0.399

Asia WGS AF: 0.511 AC: 1776 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	-0.87
CADD	Benign	3.8
DANN	Benign	0.62
PhyloP100		-0.85
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: rs2292699; hg19: chr17-45362295;