3-37782209-T-C

Variant names:

• chr3-37782209-T-C
• rs3845948
• NM_002207.3:c.2787+2188T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.2787+2188T>C		intron_variant	Intron 25 of 27	ENST00000264741.10	NP_002198.2
ITGA9-AS1	NR_110531.1	n.257-28157A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA9	ENST00000264741.10	c.2787+2188T>C		intron_variant	Intron 25 of 27	1	NM_002207.3	ENSP00000264741.5

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

African (AFR) AF: 0.304 AC: 12599 AN: 41508

American (AMR) AF: 0.173 AC: 2642 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3472

East Asian (EAS) AF: 0.478 AC: 2473 AN: 5176

South Asian (SAS) AF: 0.114 AC: 549 AN: 4832

European-Finnish (FIN) AF: 0.198 AC: 2098 AN: 10604

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14234 AN: 68002

Other (OTH) AF: 0.211 AC: 447 AN: 2116

Alfa AF: 0.217 Hom.: 1240

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
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3845948; hg19: chr3-37823700;