3-37782209-T-C

Variant summary

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

The NM_002207.3(ITGA9):c.2787+2188T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,208 control chromosomes in the GnomAD database, including 4,548 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 0.23 (4548 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

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]

ITGA9-AS1 (HGNC:49668): (ITGA9 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA9	NM_002207.3	c.2787+2188T>C		intron_variant		ENST00000264741.10
ITGA9-AS1	NR_110531.1	n.257-28157A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA9	ENST00000264741.10	c.2787+2188T>C		intron_variant		1	NM_002207.3	P1
ITGA9-AS1	ENST00000653023.1	n.335+26495A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35540 AN: 152090 Hom.: 4550 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.234 AC: 35556 AN: 152208 Hom.: 4548 Cov.: 33 AF XY: 0.229 AC XY: 17077 AN XY: 74424

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.211

Alfa AF: 0.215 Hom.: 1199

Bravo AF: 0.237

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.9
Dann	Benign	0.82

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: rs3845948; hg19: chr3-37823700;