2-186638254-A-ATTTG
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_002210.5(ITGAV):c.803-7_803-4dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,610,768 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
ITGAV
NM_002210.5 intron
NM_002210.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.51
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 2-186638254-A-ATTTG is Benign according to our data. Variant chr2-186638254-A-ATTTG is described in ClinVar as [Likely_benign]. Clinvar id is 3047661.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 17 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAV | NM_002210.5 | c.803-7_803-4dup | intron_variant | ENST00000261023.8 | |||
ITGAV | NM_001144999.3 | c.665-7_665-4dup | intron_variant | ||||
ITGAV | NM_001145000.3 | c.695-7_695-4dup | intron_variant | ||||
ITGAV | XM_047444225.1 | c.-41-7_-41-4dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAV | ENST00000261023.8 | c.803-7_803-4dup | intron_variant | 1 | NM_002210.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152172Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000121 AC: 30AN: 247956Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134082
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GnomAD4 exome AF: 0.000137 AC: 200AN: 1458478Hom.: 0 Cov.: 30 AF XY: 0.000128 AC XY: 93AN XY: 725576
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ITGAV-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 27, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at