rs11129773

Variant names:

• chr3-37813623-C-T
• rs11129773
• NM_002207.3:c.3010-5268C>T

Variant summary

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

The NM_002207.3(ITGA9):​c.3010-5268C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,214 control chromosomes in the GnomAD database, including 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 0.042 (170 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• 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]

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 (NFE) allele frequency at 95% confidence interval = 0.0596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.3010-5268C>T		intron_variant	Intron 27 of 27	ENST00000264741.10	NP_002198.2
ITGA9-AS1	NR_110531.1	n.256+7391G>A		intron_variant	Intron 3 of 3
ITGA9-AS1	NR_110532.1	n.325+7391G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA9	ENST00000264741.10	c.3010-5268C>T		intron_variant	Intron 27 of 27	1	NM_002207.3	ENSP00000264741.5

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6345 AN: 152096 Hom.: 170 Cov.: 33

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0417 AC: 6352 AN: 152214 Hom.: 170 Cov.: 33 AF XY: 0.0403 AC XY: 3002 AN XY: 74412

African (AFR) AF: 0.0213 AC: 883 AN: 41552

American (AMR) AF: 0.0432 AC: 661 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3468

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4828

European-Finnish (FIN) AF: 0.0191 AC: 202 AN: 10598

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0612 AC: 4159 AN: 67982

Other (OTH) AF: 0.0421 AC: 89 AN: 2112

Alfa AF: 0.0523 Hom.: 277

Bravo AF: 0.0436

Asia WGS AF: 0.0210 AC: 72 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	0.92
DANN	Benign	0.52
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism

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: rs11129773; hg19: chr3-37855114;