rs6550503

Variant names:

• chr3-37731182-T-A
• rs6550503
• NM_002207.3:c.2068-1530T>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.2068-1530T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,036 control chromosomes in the GnomAD database, including 20,263 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 0.51 (20263 hom., cov: 32)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.2068-1530T>A		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.2068-1530T>A		intron_variant	Intron 18 of 27	1	NM_002207.3	ENSP00000264741.5

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77904 AN: 151918 Hom.: 20255 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.513 AC: 77956 AN: 152036 Hom.: 20263 Cov.: 32 AF XY: 0.512 AC XY: 38039 AN XY: 74334

African (AFR) AF: 0.582 AC: 24126 AN: 41472

American (AMR) AF: 0.514 AC: 7858 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1525 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2350 AN: 5168

South Asian (SAS) AF: 0.569 AC: 2737 AN: 4808

European-Finnish (FIN) AF: 0.463 AC: 4893 AN: 10572

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32991 AN: 67952

Other (OTH) AF: 0.493 AC: 1041 AN: 2110

Alfa AF: 0.504 Hom.: 2420

Bravo AF: 0.517

Asia WGS AF: 0.524 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.59
DANN	Benign	0.21
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: rs6550503; hg19: chr3-37772673;