2-160111876-G-A

Position:

• chr2-160111876-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000888.5(ITGB6):​c.2101+204C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,936 control chromosomes in the GnomAD database, including 3,209 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.20 (3209 hom., cov: 31)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.307

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 2-160111876-G-A is Benign according to our data. Variant chr2-160111876-G-A is described in ClinVar as [Benign]. Clinvar id is 1226997.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB6	NM_000888.5	c.2101+204C>T		intron_variant		ENST00000283249.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB6	ENST00000283249.7	c.2101+204C>T		intron_variant		1	NM_000888.5	P1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29663 AN: 151820 Hom.: 3189 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.196 AC: 29712 AN: 151936 Hom.: 3209 Cov.: 31 AF XY: 0.195 AC XY: 14497 AN XY: 74260

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.203

Alfa AF: 0.181 Hom.: 337

Bravo AF: 0.211

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs72977408; hg19: chr2-160968387;