3-37702477-T-C

Variant names:

• chr3-37702477-T-C
• rs743393
• NM_002207.3:c.2067+18462T>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+18462T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,010 control chromosomes in the GnomAD database, including 38,931 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 0.71 (38931 hom., cov: 31)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.2067+18462T>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+18462T>C		intron_variant	Intron 18 of 27	1	NM_002207.3	ENSP00000264741.5

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107651 AN: 151892 Hom.: 38895 Cov.: 31

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.709 AC: 107745 AN: 152010 Hom.: 38931 Cov.: 31 AF XY: 0.710 AC XY: 52743 AN XY: 74292

African (AFR) AF: 0.852 AC: 35337 AN: 41476

American (AMR) AF: 0.619 AC: 9451 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1944 AN: 3464

East Asian (EAS) AF: 0.654 AC: 3367 AN: 5146

South Asian (SAS) AF: 0.835 AC: 4014 AN: 4808

European-Finnish (FIN) AF: 0.679 AC: 7180 AN: 10580

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44362 AN: 67954

Other (OTH) AF: 0.665 AC: 1402 AN: 2108

Alfa AF: 0.664 Hom.: 62211

Bravo AF: 0.703

Asia WGS AF: 0.743 AC: 2584 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.72
PhyloP100		-1.2
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: rs743393; hg19: chr3-37743968;