Genetic Variant ITGA9:p.Arg12Gly (chr3-37452408-A-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002207.3(ITGA9):c.34A>G(p.Arg12Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R12R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ITGA9
NM_002207.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.930

Publications

0 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.090224326).

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.34A>G	p.Arg12Gly	missense	Exon 1 of 28	NP_002198.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ITGA9	ENST00000264741.10	TSL:1 MANE Select	c.34A>G	p.Arg12Gly	missense	Exon 1 of 28	ENSP00000264741.5	Q13797
ITGA9	ENST00000422441.5	TSL:1	c.34A>G	p.Arg12Gly	missense	Exon 1 of 16	ENSP00000397258.1	E9PDS3
ITGA9	ENST00000921363.1		c.34A>G	p.Arg12Gly	missense	Exon 1 of 28	ENSP00000591422.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1266792

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

623772

African (AFR)

AF:

0.00

AC:

AN:

25158

American (AMR)

AF:

0.00

AC:

AN:

20936

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20526

East Asian (EAS)

AF:

0.00

AC:

AN:

26002

South Asian (SAS)

AF:

0.00

AC:

AN:

65894

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38350

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3644

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1015184

Other (OTH)

AF:

0.00

AC:

AN:

51098

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.045

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.47

DEOGEN2

Benign

0.011

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.97

FATHMM_MKL

Benign

0.020

LIST_S2

Benign

0.32

M_CAP

Benign

0.085

MetaRNN

Benign

0.090

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.0

PhyloP100

0.93

PrimateAI

Pathogenic

0.84

PROVEAN

Benign

0.63

REVEL

Benign

0.074

Sift

Benign

0.58

Sift4G

Benign

0.57

Polyphen

0.0

Vest4

0.12

MutPred

0.51

Loss of methylation at R12 (P = 0.006)

MVP

0.35

MPC

1.9

ClinPred

0.070

GERP RS

1.2

PromoterAI

0.054

Neutral

(source)

Varity_R

0.073

gMVP

0.37

Mutation Taster

=92/8

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over