3-37562521-T-G

Variant names:

• chr3-37562521-T-G
• rs9825420
• NM_002207.3:c.1689+19936T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002207.3(ITGA9):​c.1689+19936T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,172 control chromosomes in the GnomAD database, including 3,170 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 0.17 (3170 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 5 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]

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 (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002207.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA9	NM_002207.3	MANE Select	c.1689+19936T>G		intron	N/A	NP_002198.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA9	ENST00000264741.10	TSL:1 MANE Select	c.1689+19936T>G		intron	N/A	ENSP00000264741.5	Q13797
	ITGA9	ENST00000422441.5	TSL:1	c.1689+19936T>G		intron	N/A	ENSP00000397258.1	E9PDS3
	ITGA9	ENST00000921363.1		c.1689+19936T>G		intron	N/A	ENSP00000591422.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26494 AN: 152054 Hom.: 3151 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0945

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.175 AC: 26555 AN: 152172 Hom.: 3170 Cov.: 33 AF XY: 0.169 AC XY: 12562 AN XY: 74402

African (AFR) AF: 0.341 AC: 14121 AN: 41466

American (AMR) AF: 0.108 AC: 1659 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3470

East Asian (EAS) AF: 0.0573 AC: 297 AN: 5182

South Asian (SAS) AF: 0.0738 AC: 356 AN: 4824

European-Finnish (FIN) AF: 0.0945 AC: 1002 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8249 AN: 68004

Other (OTH) AF: 0.154 AC: 325 AN: 2114

Alfa AF: 0.130 Hom.: 3492

Bravo AF: 0.183

Asia WGS AF: 0.0880 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		0.17
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: rs9825420; hg19: chr3-37604012;