rs10174098

Variant names:

• chr2-186628015-G-A
• rs10174098
• NM_002210.5:c.523+2428G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-186628015-G-A
• chr2-186628015-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002210.5(ITGAV):​c.523+2428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,840 control chromosomes in the GnomAD database, including 30,004 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 0.62 (30004 hom., cov: 31)
• Consequence: ITGAV NM_002210.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 13 publications found

Genes affected

ITGAV (HGNC:6150): (integrin subunit alpha V) The product of this gene belongs to the integrin alpha chain family. Integrins are heterodimeric integral membrane proteins composed of an alpha subunit and a beta subunit that function in cell surface adhesion and signaling. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha V subunit. This subunit associates with beta 1, beta 3, beta 5, beta 6 and beta 8 subunits. The heterodimer consisting of alpha V and beta 3 subunits is also known as the vitronectin receptor. This integrin may regulate angiogenesis and cancer progression. Alternative splicing results in multiple transcript variants. Note that the integrin alpha 5 and integrin alpha V subunits are encoded by distinct genes. [provided by RefSeq, Oct 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGAV	NM_002210.5	c.523+2428G>A		intron_variant	Intron 4 of 29	ENST00000261023.8	NP_002201.2
ITGAV	NM_001145000.3	c.523+2428G>A		intron_variant	Intron 4 of 27		NP_001138472.2
ITGAV	NM_001144999.3	c.385+2428G>A		intron_variant	Intron 4 of 29		NP_001138471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGAV	ENST00000261023.8	c.523+2428G>A		intron_variant	Intron 4 of 29	1	NM_002210.5	ENSP00000261023.3

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94664 AN: 151722 Hom.: 29998 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.624 AC: 94700 AN: 151840 Hom.: 30004 Cov.: 31 AF XY: 0.623 AC XY: 46265 AN XY: 74224

African (AFR) AF: 0.499 AC: 20633 AN: 41390

American (AMR) AF: 0.629 AC: 9586 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3472

East Asian (EAS) AF: 0.798 AC: 4120 AN: 5160

South Asian (SAS) AF: 0.629 AC: 3027 AN: 4814

European-Finnish (FIN) AF: 0.664 AC: 6992 AN: 10530

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.676 AC: 45877 AN: 67914

Other (OTH) AF: 0.629 AC: 1328 AN: 2110

Alfa AF: 0.619 Hom.: 10393

Bravo AF: 0.617

Asia WGS AF: 0.679 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.79
PhyloP100		-0.25
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: rs10174098; hg19: chr2-187492742;