rs7636734

Variant names:

• chr3-37705360-T-C
• rs7636734
• NM_002207.3:c.2067+21345T>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.2067+21345T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,034 control chromosomes in the GnomAD database, including 25,676 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 0.58 (25676 hom., cov: 32)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.2067+21345T>C		intron_variant	Intron 18 of 27	ENST00000264741.10	NP_002198.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA9	ENST00000264741.10	c.2067+21345T>C		intron_variant	Intron 18 of 27	1	NM_002207.3	ENSP00000264741.5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87407 AN: 151916 Hom.: 25650 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.575 AC: 87490 AN: 152034 Hom.: 25676 Cov.: 32 AF XY: 0.573 AC XY: 42570 AN XY: 74302

African (AFR) AF: 0.695 AC: 28832 AN: 41484

American (AMR) AF: 0.550 AC: 8401 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1633 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2327 AN: 5154

South Asian (SAS) AF: 0.589 AC: 2835 AN: 4810

European-Finnish (FIN) AF: 0.486 AC: 5133 AN: 10560

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36666 AN: 67964

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

Alfa AF: 0.557 Hom.: 15358

Bravo AF: 0.582

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.74
PhyloP100		-0.35
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: rs7636734; hg19: chr3-37746851;