2-160101634-T-C

Position:

• chr2-160101634-T-C

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.*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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.230

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=-0.47).
• 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_single_submitter, 1 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	UniProt
ITGB6	NM_000888.5	c.*102A>G		3_prime_UTR_variant	15/15	ENST00000283249.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB6	ENST00000283249.7	c.*102A>G		3_prime_UTR_variant	15/15	1	NM_000888.5	P1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23416 AN: 152080 Hom.: 2425 Cov.: 32

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.: 7 AF XY: 0.176 AC XY: 55416 AN XY: 314952

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.: 32 AF XY: 0.150 AC XY: 11143 AN XY: 74394

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: 95 AN: 3474

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	-0.47
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

Other links and lift over

dbSNP: rs7586751; hg19: chr2-160958145; COSMIC: COSV51791329; COSMIC: COSV51791329;