3-37548944-T-C

Variant names:

• chr3-37548944-T-C
• rs166508
• NM_002207.3:c.1689+6359T>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.1689+6359T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,058 control chromosomes in the GnomAD database, including 15,885 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 0.44 (15885 hom., cov: 32)
• Consequence: ITGA9 NM_002207.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA9	NM_002207.3	c.1689+6359T>C		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+6359T>C		intron_variant	Intron 15 of 27	1	NM_002207.3	ENSP00000264741.5
ITGA9	ENST00000422441.5	c.1689+6359T>C		intron_variant	Intron 15 of 15	1		ENSP00000397258.1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67511 AN: 151940 Hom.: 15874 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.444 AC: 67545 AN: 152058 Hom.: 15885 Cov.: 32 AF XY: 0.442 AC XY: 32885 AN XY: 74328

African (AFR) AF: 0.319 AC: 13252 AN: 41484

American (AMR) AF: 0.538 AC: 8213 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1574 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3699 AN: 5170

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4816

European-Finnish (FIN) AF: 0.467 AC: 4936 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32648 AN: 67958

Other (OTH) AF: 0.429 AC: 905 AN: 2110

Alfa AF: 0.452 Hom.: 1975

Bravo AF: 0.453

Asia WGS AF: 0.509 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.7
DANN	Benign	0.56
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: rs166508; hg19: chr3-37590435;