3-37474336-A-G

Variant names:

• chr3-37474336-A-G
• rs197770
• NM_002207.3:c.420+876A>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.420+876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,272 control chromosomes in the GnomAD database, including 1,237 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 0.12 (1237 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 10 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.420+876A>G		intron_variant	Intron 3 of 27	ENST00000264741.10	NP_002198.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA9	ENST00000264741.10	c.420+876A>G		intron_variant	Intron 3 of 27	1	NM_002207.3	ENSP00000264741.5
ITGA9	ENST00000422441.5	c.420+876A>G		intron_variant	Intron 3 of 15	1		ENSP00000397258.1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17622 AN: 152156 Hom.: 1231 Cov.: 33

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0589

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.116 AC: 17657 AN: 152272 Hom.: 1237 Cov.: 33 AF XY: 0.116 AC XY: 8621 AN XY: 74450

African (AFR) AF: 0.0483 AC: 2008 AN: 41570

American (AMR) AF: 0.158 AC: 2417 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3472

East Asian (EAS) AF: 0.0592 AC: 307 AN: 5182

South Asian (SAS) AF: 0.108 AC: 523 AN: 4826

European-Finnish (FIN) AF: 0.140 AC: 1484 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10154 AN: 68012

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.137 Hom.: 6574

Bravo AF: 0.114

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.39
PhyloP100		-3.2
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: rs197770; hg19: chr3-37515827;