3-37570369-C-T

Variant names:

• chr3-37570369-C-T
• rs2844363
• NM_002207.3:c.1689+27784C>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.1689+27784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,050 control chromosomes in the GnomAD database, including 23,310 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 0.55 (23310 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• 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]

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 = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002207.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA9	NM_002207.3	MANE Select	c.1689+27784C>T		intron	N/A	NP_002198.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA9	ENST00000264741.10	TSL:1 MANE Select	c.1689+27784C>T		intron	N/A	ENSP00000264741.5	Q13797
	ITGA9	ENST00000422441.5	TSL:1	c.1689+27784C>T		intron	N/A	ENSP00000397258.1	E9PDS3
	ITGA9	ENST00000921363.1		c.1689+27784C>T		intron	N/A	ENSP00000591422.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83498 AN: 151932 Hom.: 23283 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.550 AC: 83581 AN: 152050 Hom.: 23310 Cov.: 33 AF XY: 0.546 AC XY: 40580 AN XY: 74334

African (AFR) AF: 0.533 AC: 22068 AN: 41442

American (AMR) AF: 0.565 AC: 8642 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1786 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2501 AN: 5174

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4814

European-Finnish (FIN) AF: 0.598 AC: 6318 AN: 10572

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39022 AN: 67982

Other (OTH) AF: 0.531 AC: 1121 AN: 2110

Alfa AF: 0.558 Hom.: 37149

Bravo AF: 0.549

Asia WGS AF: 0.424 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.82
PhyloP100		-0.21
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: rs2844363; hg19: chr3-37611860;