chr2-186625505-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002210.5(ITGAV):c.441G>A(p.Glu147=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00149 in 1,614,010 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0082 ( 18 hom., cov: 31)
Exomes 𝑓: 0.00079 ( 16 hom. )
Consequence
ITGAV
NM_002210.5 synonymous
NM_002210.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.20
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
Variant 2-186625505-G-A is Benign according to our data. Variant chr2-186625505-G-A is described in ClinVar as [Benign]. Clinvar id is 787777.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.2 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00818 (1246/152290) while in subpopulation AFR AF= 0.028 (1165/41546). AF 95% confidence interval is 0.0267. There are 18 homozygotes in gnomad4. There are 584 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1244 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAV | NM_002210.5 | c.441G>A | p.Glu147= | synonymous_variant | 4/30 | ENST00000261023.8 | |
ITGAV | NM_001145000.3 | c.441G>A | p.Glu147= | synonymous_variant | 4/28 | ||
ITGAV | NM_001144999.3 | c.303G>A | p.Glu101= | synonymous_variant | 4/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAV | ENST00000261023.8 | c.441G>A | p.Glu147= | synonymous_variant | 4/30 | 1 | NM_002210.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00817 AC: 1244AN: 152172Hom.: 18 Cov.: 31
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GnomAD3 exomes AF: 0.00216 AC: 544AN: 251312Hom.: 4 AF XY: 0.00157 AC XY: 213AN XY: 135818
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GnomAD4 exome AF: 0.000795 AC: 1162AN: 1461720Hom.: 16 Cov.: 31 AF XY: 0.000653 AC XY: 475AN XY: 727168
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 18, 2018 | - - |
Computational scores
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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