3-37520650-G-A

Variant names:

• chr3-37520650-G-A
• rs155524
• NM_002207.3:c.1236+1296G>A

Variant summary

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

The NM_002207.3(ITGA9):​c.1236+1296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,130 control chromosomes in the GnomAD database, including 30,710 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 0.63 (30710 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 16 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]

ENSG00000309482 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA9	NM_002207.3	MANE Select	c.1236+1296G>A		intron	N/A	NP_002198.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA9	ENST00000264741.10	TSL:1 MANE Select	c.1236+1296G>A		intron	N/A	ENSP00000264741.5
	ITGA9	ENST00000422441.5	TSL:1	c.1236+1296G>A		intron	N/A	ENSP00000397258.1
	ENSG00000309482	ENST00000841368.1		n.86+1059C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95795 AN: 152012 Hom.: 30664 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.630 AC: 95894 AN: 152130 Hom.: 30710 Cov.: 33 AF XY: 0.630 AC XY: 46854 AN XY: 74370

African (AFR) AF: 0.696 AC: 28874 AN: 41498

American (AMR) AF: 0.671 AC: 10266 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1828 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4442 AN: 5166

South Asian (SAS) AF: 0.607 AC: 2930 AN: 4824

European-Finnish (FIN) AF: 0.591 AC: 6246 AN: 10574

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.579 AC: 39345 AN: 67982

Other (OTH) AF: 0.603 AC: 1271 AN: 2108

Alfa AF: 0.593 Hom.: 14514

Bravo AF: 0.645

Asia WGS AF: 0.712 AC: 2478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		0.77
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: rs155524; hg19: chr3-37562141;