Variant chr2-160101838-GA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000888.5(ITGB6):c.2269-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 29163 hom., cov: 0)

Exomes 𝑓: 0.55 ( 96160 hom. )

Failed GnomAD Quality Control

Consequence

ITGB6
NM_000888.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.917

Variant links:

Genes affected

ITGB6 (HGNC:6161): (integrin subunit beta 6) This gene encodes a protein that is a member of the integrin superfamily. Members of this family are adhesion receptors that function in signaling from the extracellular matrix to the cell. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. The encoded protein forms a dimer with an alpha v chain and this heterodimer can bind to ligands like fibronectin and transforming growth factor beta 1. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ITGB6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 2-160101838-GA-G is Benign according to our data. Variant chr2-160101838-GA-G is described in ClinVar as [Benign]. Clinvar id is 218475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB6	NM_000888.5 linkuse as main transcript	c.2269-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000283249.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB6	ENST00000283249.7 linkuse as main transcript	c.2269-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_000888.5	P1	P18564-1

Frequencies

GnomAD3 genomes

AF:

0.571

AC:

85718

AN:

150220

Hom.:

29162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.851

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.710

Gnomad EAS

AF:

0.539

Gnomad SAS

AF:

0.618

Gnomad FIN

AF:

0.770

Gnomad MID

AF:

0.715

Gnomad NFE

AF:

0.765

Gnomad OTH

AF:

0.603

GnomAD3 exomes

AF:

0.509

AC:

82719

AN:

162560

Hom.:

14857

AF XY:

0.520

AC XY:

44878

AN XY:

86300

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.389

Gnomad ASJ exome

AF:

0.531

Gnomad EAS exome

AF:

0.443

Gnomad SAS exome

AF:

0.488

Gnomad FIN exome

AF:

0.613

Gnomad NFE exome

AF:

0.598

Gnomad OTH exome

AF:

0.529

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.549

AC:

529515

AN:

964114

Hom.:

96160

Cov.:

AF XY:

0.550

AC XY:

270894

AN XY:

492450

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.387

Gnomad4 ASJ exome

AF:

0.538

Gnomad4 EAS exome

AF:

0.445

Gnomad4 SAS exome

AF:

0.498

Gnomad4 FIN exome

AF:

0.591

Gnomad4 NFE exome

AF:

0.579

Gnomad4 OTH exome

AF:

0.529

GnomAD4 genome

AF:

0.570

AC:

85714

AN:

150330

Hom.:

29163

Cov.:

AF XY:

0.571

AC XY:

41851

AN XY:

73308

show subpopulations

Gnomad4 AFR

AF:

0.191

Gnomad4 AMR

AF:

0.544

Gnomad4 ASJ

AF:

0.710

Gnomad4 EAS

AF:

0.540

Gnomad4 SAS

AF:

0.618

Gnomad4 FIN

AF:

0.770

Gnomad4 NFE

AF:

0.765

Gnomad4 OTH

AF:

0.602

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

Apr 17, 2015

- -

Amelogenesis imperfecta type 1H

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 19, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 09, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over