rs2212020

Variant names:

• chr3-37475971-C-T
• rs2212020
• NM_002207.3:c.420+2511C>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.420+2511C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,084 control chromosomes in the GnomAD database, including 8,931 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 0.34 (8931 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.420+2511C>T		intron_variant	Intron 3 of 27	ENST00000264741.10	NP_002198.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA9	ENST00000264741.10	c.420+2511C>T		intron_variant	Intron 3 of 27	1	NM_002207.3	ENSP00000264741.5
ITGA9	ENST00000422441.5	c.420+2511C>T		intron_variant	Intron 3 of 15	1		ENSP00000397258.1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51657 AN: 151966 Hom.: 8926 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.340 AC: 51703 AN: 152084 Hom.: 8931 Cov.: 33 AF XY: 0.335 AC XY: 24880 AN XY: 74376

African (AFR) AF: 0.345 AC: 14287 AN: 41458

American (AMR) AF: 0.349 AC: 5332 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3468

East Asian (EAS) AF: 0.146 AC: 759 AN: 5188

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4824

European-Finnish (FIN) AF: 0.308 AC: 3255 AN: 10558

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24465 AN: 67976

Other (OTH) AF: 0.344 AC: 726 AN: 2110

Alfa AF: 0.356 Hom.: 16167

Bravo AF: 0.346

Asia WGS AF: 0.197 AC: 686 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	7.3
DANN	Benign	0.56
PhyloP100		0.41
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: rs2212020; hg19: chr3-37517462;