2-186638499-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002210.5(ITGAV):c.903+34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 1,552,480 control chromosomes in the GnomAD database, including 129,488 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 0.43 ( 14539 hom., cov: 32)
Exomes 𝑓: 0.40 ( 114949 hom. )
Consequence
ITGAV
NM_002210.5 intron
NM_002210.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.826
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAV | NM_002210.5 | c.903+34T>C | intron_variant | ENST00000261023.8 | |||
ITGAV | NM_001144999.3 | c.765+34T>C | intron_variant | ||||
ITGAV | NM_001145000.3 | c.795+34T>C | intron_variant | ||||
ITGAV | XM_047444225.1 | c.60+34T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAV | ENST00000261023.8 | c.903+34T>C | intron_variant | 1 | NM_002210.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.431 AC: 65501AN: 151838Hom.: 14518 Cov.: 32
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GnomAD3 exomes AF: 0.438 AC: 108659AN: 247880Hom.: 25511 AF XY: 0.427 AC XY: 57343AN XY: 134306
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GnomAD4 exome AF: 0.397 AC: 555476AN: 1400524Hom.: 114949 Cov.: 23 AF XY: 0.394 AC XY: 275756AN XY: 700244
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GnomAD4 genome ? AF: 0.432 AC: 65572AN: 151956Hom.: 14539 Cov.: 32 AF XY: 0.438 AC XY: 32531AN XY: 74256
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at