rs189897

chr3-37477054-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002207.3(ITGA9):c.420+3594T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,228 control chromosomes in the GnomAD database, including 1,717 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1717 hom., cov: 32)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

Genes affected

ITGA9 (HGNC:6145): (integrin subunit alpha 9) This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane glycoproteins composed of an alpha chain and a beta chain that mediate cell-cell and cell-matrix adhesion. The protein encoded by this gene, when bound to the beta 1 chain, forms an integrin that is a receptor for VCAM1, cytotactin and osteopontin. Expression of this gene has been found to be upregulated in small cell lung cancers. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA9	NM_002207.3	c.420+3594T>A		intron_variant		ENST00000264741.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA9	ENST00000264741.10	c.420+3594T>A		intron_variant		1	NM_002207.3	P1
ITGA9	ENST00000422441.5	c.420+3594T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20475 AN: 152110 Hom.: 1715 Cov.: 32

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.135 AC: 20490 AN: 152228 Hom.: 1717 Cov.: 32 AF XY: 0.132 AC XY: 9850 AN XY: 74402

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0671

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.144

Alfa AF: 0.169 Hom.: 1291

Bravo AF: 0.131

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.023
Dann	Benign	0.37

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: rs189897; hg19: chr3-37518545;