rs9333289
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000261023.8(ITGAV):c.631+6T>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ITGAV
ENST00000261023.8 splice_donor_region, intron
ENST00000261023.8 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.6056
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.675
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGAV | NM_002210.5 | c.631+6T>A | splice_donor_region_variant, intron_variant | ENST00000261023.8 | NP_002201.2 | |||
ITGAV | NM_001144999.3 | c.493+6T>A | splice_donor_region_variant, intron_variant | NP_001138471.2 | ||||
ITGAV | NM_001145000.3 | c.524-2702T>A | intron_variant | NP_001138472.2 | ||||
ITGAV | XM_047444225.1 | c.-213+6T>A | splice_donor_region_variant, intron_variant | XP_047300181.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGAV | ENST00000261023.8 | c.631+6T>A | splice_donor_region_variant, intron_variant | 1 | NM_002210.5 | ENSP00000261023 | P2 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
Cov.:
30
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1394266Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 696168
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1394266
Hom.:
Cov.:
21
AF XY:
AC XY:
0
AN XY:
696168
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 30
GnomAD4 genome
Cov.:
30
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
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