2-186622433-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_002210.5(ITGAV):c.408+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 1,591,498 control chromosomes in the GnomAD database, including 444,592 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 0.75 ( 43295 hom., cov: 31)
Exomes 𝑓: 0.75 ( 401297 hom. )
Consequence
ITGAV
NM_002210.5 splice_donor_region, intron
NM_002210.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00002264
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.30
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAV | NM_002210.5 | c.408+3G>A | splice_donor_region_variant, intron_variant | ENST00000261023.8 | |||
ITGAV | NM_001144999.3 | c.270+3G>A | splice_donor_region_variant, intron_variant | ||||
ITGAV | NM_001145000.3 | c.408+3G>A | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAV | ENST00000261023.8 | c.408+3G>A | splice_donor_region_variant, intron_variant | 1 | NM_002210.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.754 AC: 114643AN: 151950Hom.: 43258 Cov.: 31
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GnomAD3 exomes AF: 0.746 AC: 187310AN: 251098Hom.: 70118 AF XY: 0.746 AC XY: 101302AN XY: 135734
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GnomAD4 exome AF: 0.746 AC: 1073721AN: 1439430Hom.: 401297 Cov.: 26 AF XY: 0.745 AC XY: 534642AN XY: 717604
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GnomAD4 genome AF: 0.755 AC: 114739AN: 152068Hom.: 43295 Cov.: 31 AF XY: 0.754 AC XY: 56022AN XY: 74332
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at