rs1800

Variant names:

• chr3-37764371-T-C
• rs1800
• NM_002207.3:c.2542-13021T>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.2542-13021T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 150,288 control chromosomes in the GnomAD database, including 9,667 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 0.35 (9667 hom., cov: 29)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 12 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.2542-13021T>C		intron_variant	Intron 23 of 27	ENST00000264741.10	NP_002198.2
ITGA9-AS1	NR_110531.1	n.257-10319A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA9	ENST00000264741.10	c.2542-13021T>C		intron_variant	Intron 23 of 27	1	NM_002207.3	ENSP00000264741.5

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52165 AN: 150170 Hom.: 9656 Cov.: 29

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.347 AC: 52215 AN: 150288 Hom.: 9667 Cov.: 29 AF XY: 0.338 AC XY: 24731 AN XY: 73174

African (AFR) AF: 0.463 AC: 18918 AN: 40818

American (AMR) AF: 0.283 AC: 4254 AN: 15012

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3462

East Asian (EAS) AF: 0.107 AC: 543 AN: 5066

South Asian (SAS) AF: 0.134 AC: 635 AN: 4756

European-Finnish (FIN) AF: 0.253 AC: 2567 AN: 10142

Middle Eastern (MID) AF: 0.489 AC: 139 AN: 284

European-Non Finnish (NFE) AF: 0.333 AC: 22572 AN: 67752

Other (OTH) AF: 0.363 AC: 757 AN: 2084

Alfa AF: 0.328 Hom.: 3119

Bravo AF: 0.359

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.58
PhyloP100		-0.86
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: rs1800; hg19: chr3-37805862;