chr17-47300459-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000212.3(ITGB3):c.1914-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 1,594,948 control chromosomes in the GnomAD database, including 5,629 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 606 hom., cov: 32)

Exomes 𝑓: 0.077 ( 5023 hom. )

Consequence

ITGB3
NM_000212.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.383

Publications

11 publications found

Variant links:

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]

ITGB3 links:

ENSG00000259753 (HGNC:):

ENSG00000259753 links:

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

EFCAB13-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 17-47300459-T-C is Benign according to our data. Variant chr17-47300459-T-C is described in CliVar as Benign. Clinvar id is 255538.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-47300459-T-C is described in CliVar as Benign. Clinvar id is 255538.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-47300459-T-C is described in CliVar as Benign. Clinvar id is 255538.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB3	NM_000212.3 link	c.1914-19T>C		intron_variant	Intron 11 of 14	ENST00000559488.7	NP_000203.2	P05106-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7 link	c.1914-19T>C		intron_variant	Intron 11 of 14	1	NM_000212.3	ENSP00000452786.2		P05106-1
ENSG00000259753	ENST00000560629.1 link	n.1878-19T>C		intron_variant	Intron 11 of 17	2		ENSP00000456711.2		H3BM21

Frequencies

GnomAD3 genomes

AF:

0.0858

AC:

13044

AN:

152098

Hom.:

605

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0968

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.0833

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.0350

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.0723

Gnomad OTH

AF:

0.0985

GnomAD2 exomes

AF:

0.0885

AC:

22219

AN:

251082

AF XY:

0.0909

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.0552

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.192

Gnomad FIN exome

AF:

0.0392

Gnomad NFE exome

AF:

0.0759

Gnomad OTH exome

AF:

0.0982

GnomAD4 exome

AF:

0.0766

AC:

110569

AN:

1442732

Hom.:

5023

Cov.:

AF XY:

0.0782

AC XY:

56235

AN XY:

718980

show subpopulations

African (AFR)

AF:

0.0931

AC:

3081

AN:

33100

American (AMR)

AF:

0.0595

AC:

2660

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

3645

AN:

26022

East Asian (EAS)

AF:

0.186

AC:

7382

AN:

39596

South Asian (SAS)

AF:

0.120

AC:

10309

AN:

85854

European-Finnish (FIN)

AF:

0.0416

AC:

2221

AN:

53326

Middle Eastern (MID)

AF:

0.162

AC:

930

AN:

5742

European-Non Finnish (NFE)

AF:

0.0685

AC:

75033

AN:

1094648

Other (OTH)

AF:

0.0888

AC:

5308

AN:

59744

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

5121

10241

15362

20482

25603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2836

5672

8508

11344

14180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0858

AC:

13055

AN:

152216

Hom.:

606

Cov.:

AF XY:

0.0852

AC XY:

6343

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0967

AC:

4016

AN:

41540

American (AMR)

AF:

0.0832

AC:

1272

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

514

AN:

3472

East Asian (EAS)

AF:

0.192

AC:

994

AN:

5172

South Asian (SAS)

AF:

0.118

AC:

571

AN:

4820

European-Finnish (FIN)

AF:

0.0350

AC:

372

AN:

10616

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0724

AC:

4924

AN:

67994

Other (OTH)

AF:

0.0970

AC:

205

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

542

1083

1625

2166

2708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0815

Hom.:

186

Bravo

AF:

0.0910

Asia WGS

AF:

0.138

AC:

481

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 12, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

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

0.039

(source)

DANN

Benign

0.27

PhyloP100

-0.38

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over