3-37556891-C-T

Variant names:

• chr3-37556891-C-T
• rs743395
• NM_002207.3:c.1689+14306C>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+14306C>T 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 151,994 control chromosomes in the GnomAD database, including 9,627 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 (9627 hom., cov: 32)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.1689+14306C>T		intron_variant	Intron 15 of 27	ENST00000264741.10	NP_002198.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA9	ENST00000264741.10	c.1689+14306C>T		intron_variant	Intron 15 of 27	1	NM_002207.3	ENSP00000264741.5
ITGA9	ENST00000422441.5	c.1689+14306C>T		intron_variant	Intron 15 of 15	1		ENSP00000397258.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52641 AN: 151876 Hom.: 9620 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.347 AC: 52671 AN: 151994 Hom.: 9627 Cov.: 32 AF XY: 0.347 AC XY: 25779 AN XY: 74290

African (AFR) AF: 0.288 AC: 11957 AN: 41466

American (AMR) AF: 0.305 AC: 4660 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1504 AN: 3468

East Asian (EAS) AF: 0.0975 AC: 504 AN: 5170

South Asian (SAS) AF: 0.398 AC: 1912 AN: 4804

European-Finnish (FIN) AF: 0.394 AC: 4151 AN: 10544

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26694 AN: 67958

Other (OTH) AF: 0.375 AC: 791 AN: 2108

Alfa AF: 0.378 Hom.: 42200

Bravo AF: 0.330

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		0.029
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: rs743395; hg19: chr3-37598382;