Variant chr2-160101634-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000888.5(ITGB6):c.*102A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 733,704 control chromosomes in the GnomAD database, including 14,027 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2423 hom., cov: 32)

Exomes 𝑓: 0.18 ( 11604 hom. )

Consequence

ITGB6
NM_000888.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.230

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 2-160101634-T-C is Benign according to our data. Variant chr2-160101634-T-C is described in ClinVar as [Benign]. Clinvar id is 1274512.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB6	NM_000888.5 linkuse as main transcript	c.*102A>G		3_prime_UTR_variant	15/15	ENST00000283249.7	NP_000879.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB6	ENST00000283249.7 linkuse as main transcript	c.*102A>G		3_prime_UTR_variant	15/15	1	NM_000888.5	ENSP00000283249	P1	P18564-1

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23416

AN:

152080

Hom.:

2425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0515

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.0958

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.0443

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.143

GnomAD4 exome

AF:

0.181

AC:

105217

AN:

581506

Hom.:

11604

Cov.:

AF XY:

0.176

AC XY:

55416

AN XY:

314952

show subpopulations

Gnomad4 AFR exome

AF:

0.0490

Gnomad4 AMR exome

AF:

0.0945

Gnomad4 ASJ exome

AF:

0.101

Gnomad4 EAS exome

AF:

0.000212

Gnomad4 SAS exome

AF:

0.0470

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.238

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.154

AC:

23410

AN:

152198

Hom.:

2423

Cov.:

AF XY:

0.150

AC XY:

11143

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0513

Gnomad4 AMR

AF:

0.117

Gnomad4 ASJ

AF:

0.0958

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.0444

Gnomad4 FIN

AF:

0.206

Gnomad4 NFE

AF:

0.237

Gnomad4 OTH

AF:

0.140

Alfa

AF:

0.145

Hom.:

450

Bravo

AF:

0.143

Asia WGS

AF:

0.0270

AC:

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

8.7

DANN

Benign

0.75

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

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