dbSNP rs16828163: ITGAV:c.2707-610G>A (chr2-186674994-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002210.5(ITGAV):c.2707-610G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,096 control chromosomes in the GnomAD database, including 2,784 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 0.19 ( 2784 hom., cov: 32)

Consequence

ITGAV
NM_002210.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.556

Publications

6 publications found

Variant links:

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]

ITGAV links:

ENSG00000227227 (HGNC:41242):

ENSG00000227227 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002210.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITGAV	NM_002210.5	MANE Select	c.2707-610G>A	intron	N/A	NP_002201.2	P06756-1
ITGAV	NM_001145000.3		c.2599-610G>A	intron	N/A	NP_001138472.2	P06756-2
ITGAV	NM_001144999.3		c.2569-610G>A	intron	N/A	NP_001138471.2	P06756-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITGAV	ENST00000261023.8	TSL:1 MANE Select	c.2707-610G>A	intron	N/A	ENSP00000261023.3	P06756-1
ITGAV	ENST00000374907.7	TSL:1	c.2599-610G>A	intron	N/A	ENSP00000364042.3	P06756-2
ITGAV	ENST00000925193.1		c.2707-595G>A	intron	N/A	ENSP00000595252.1

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28359

AN:

151978

Hom.:

2782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.0784

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.192

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

GnomAD4 genome

AF:

0.186

AC:

28362

AN:

152096

Hom.:

2784

Cov.:

AF XY:

0.184

AC XY:

13699

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.155

AC:

6418

AN:

41490

American (AMR)

AF:

0.181

AC:

2765

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

560

AN:

3468

East Asian (EAS)

AF:

0.0780

AC:

404

AN:

5180

South Asian (SAS)

AF:

0.174

AC:

840

AN:

4818

European-Finnish (FIN)

AF:

0.191

AC:

2011

AN:

10540

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.217

AC:

14731

AN:

67994

Other (OTH)

AF:

0.191

AC:

403

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1182

2364

3546

4728

5910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.203

Hom.:

5089

Bravo

AF:

0.185

Asia WGS

AF:

0.158

AC:

547

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.71

(source)

DANN

Benign

0.36

PhyloP100

-0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over