rs145968481

Variant names:

• chr3-37506010-G-A
• rs145968481
• NM_002207.3:c.753G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-37506010-G-A
• chr3-37506010-G-C

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BS1 BS2

The NM_002207.3(ITGA9):​c.753G>A​(p.Val251Val) variant causes a synonymous change. The variant allele was found at a frequency of 0.00124 in 1,606,260 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0064 (9 hom., cov: 32)
  • Exomes 𝑓: 0.00069 (17 hom.)
• Consequence: ITGA9 NM_002207.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.68
• Publications: 0 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 -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BP6: Variant 3-37506010-G-A is Benign according to our data. Variant chr3-37506010-G-A is described in ClinVar as Benign. ClinVar VariationId is 697425.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00645 (981/152150) while in subpopulation AFR AF = 0.0226 (939/41502). AF 95% confidence interval is 0.0214. There are 9 homozygotes in GnomAd4. There are 471 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 gene

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.753G>A	p.Val251Val	synonymous	Exon 7 of 28	NP_002198.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA9	ENST00000264741.10	TSL:1 MANE Select	c.753G>A	p.Val251Val	synonymous	Exon 7 of 28	ENSP00000264741.5	Q13797
	ITGA9	ENST00000422441.5	TSL:1	c.753G>A	p.Val251Val	synonymous	Exon 7 of 16	ENSP00000397258.1	E9PDS3
	ITGA9	ENST00000921363.1		c.753G>A	p.Val251Val	synonymous	Exon 7 of 28	ENSP00000591422.1

Frequencies

GnomAD3 genomes AF: 0.00643 AC: 978 AN: 152032 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00288

GnomAD2 exomes AF: 0.00159 AC: 380 AN: 238408 AF XY: 0.00120

Gnomad AFR exome AF: 0.0226

Gnomad AMR exome AF: 0.000842

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000278

Gnomad OTH exome AF: 0.000854

GnomAD4 exome AF: 0.000690 AC: 1003 AN: 1454110 Hom.: 17 Cov.: 31 AF XY: 0.000616 AC XY: 445 AN XY: 722264

African (AFR) AF: 0.0241 AC: 806 AN: 33396

American (AMR) AF: 0.000984 AC: 43 AN: 43690

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25910

East Asian (EAS) AF: 0.0000253 AC: 1 AN: 39538

South Asian (SAS) AF: 0.000190 AC: 16 AN: 84166

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52924

Middle Eastern (MID) AF: 0.000694 AC: 4 AN: 5762

European-Non Finnish (NFE) AF: 0.0000189 AC: 21 AN: 1108604

Other (OTH) AF: 0.00186 AC: 112 AN: 60120

GnomAD4 genome AF: 0.00645 AC: 981 AN: 152150 Hom.: 9 Cov.: 32 AF XY: 0.00633 AC XY: 471 AN XY: 74390

African (AFR) AF: 0.0226 AC: 939 AN: 41502

American (AMR) AF: 0.00216 AC: 33 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10584

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68018

Other (OTH) AF: 0.00285 AC: 6 AN: 2106

Alfa AF: 0.00228 Hom.: 4

Bravo AF: 0.00740

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	4.1
DANN	Benign	0.82
PhyloP100		3.7
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs145968481; hg19: chr3-37547501;