rs267567

Positions:

• chr3-37532533-G-A
• chr3-37532533-G-C
• chr3-37532533-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002207.3(ITGA9):​c.1374-781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,094 control chromosomes in the GnomAD database, including 13,042 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 0.38 (13042 hom., cov: 33)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA9	NM_002207.3	c.1374-781G>A		intron_variant		ENST00000264741.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA9	ENST00000264741.10	c.1374-781G>A		intron_variant		1	NM_002207.3	P1
ITGA9	ENST00000422441.5	c.1374-781G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58342 AN: 151976 Hom.: 13034 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.384 AC: 58371 AN: 152094 Hom.: 13042 Cov.: 33 AF XY: 0.384 AC XY: 28531 AN XY: 74342

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.376

Alfa AF: 0.431 Hom.: 7644

Bravo AF: 0.385

Asia WGS AF: 0.488 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs267567; hg19: chr3-37574024;