17-50063970-G-A

Variant summary

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

The NM_002204.4(ITGA3):c.207-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,443,118 control chromosomes in the GnomAD database, including 12,075 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1526 hom., cov: 32)
  • Exomes 𝑓: 0.11 (10549 hom.)
• Consequence: ITGA3 NM_002204.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.13

Genes affected

ITGA3 (HGNC:6139): (integrin subunit alpha 3) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function as cell surface adhesion molecules. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 3 subunit. This subunit joins with a beta 1 subunit to form an integrin that interacts with extracellular matrix proteins including members of the laminin family. Expression of this gene may be correlated with breast cancer metastasis. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 17-50063970-G-A is Benign according to our data. Variant chr17-50063970-G-A is described in ClinVar as [Benign]. Clinvar id is 1242445.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA3	NM_002204.4	c.207-107G>A		intron_variant		ENST00000320031.13
ITGA3	XM_005257308.3	c.207-107G>A		intron_variant
ITGA3	XM_047435922.1	c.207-107G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA3	ENST00000320031.13	c.207-107G>A		intron_variant		1	NM_002204.4	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19023 AN: 151964 Hom.: 1518 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.109 AC: 140174 AN: 1291036 Hom.: 10549 Cov.: 20 AF XY: 0.111 AC XY: 70692 AN XY: 634106

Gnomad4 AFR exome AF: 0.111

Gnomad4 AMR exome AF: 0.315

Gnomad4 ASJ exome AF: 0.108

Gnomad4 EAS exome AF: 0.335

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.0979

Gnomad4 NFE exome AF: 0.0845

Gnomad4 OTH exome AF: 0.122

GnomAD4 genome AF: 0.125 AC: 19059 AN: 152082 Hom.: 1526 Cov.: 32 AF XY: 0.132 AC XY: 9784 AN XY: 74324

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.0988

Gnomad4 NFE AF: 0.0882

Gnomad4 OTH AF: 0.136

Alfa AF: 0.107 Hom.: 115

Bravo AF: 0.135

Asia WGS AF: 0.298 AC: 1036 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

Nov 12, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.91
Dann	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs55827079; hg19: chr17-48141334; COSMIC: COSV50337682;