rs5030341
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_000201.3(ICAM1):c.67+1373_67+1374delCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 7750 hom., cov: 0)
Consequence
ICAM1
NM_000201.3 intron
NM_000201.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0780
Genes affected
ICAM1 (HGNC:5344): (intercellular adhesion molecule 1) This gene encodes a cell surface glycoprotein which is typically expressed on endothelial cells and cells of the immune system. It binds to integrins of type CD11a / CD18, or CD11b / CD18 and is also exploited by Rhinovirus as a receptor. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ICAM1 | NM_000201.3 | c.67+1373_67+1374delCT | intron_variant | ENST00000264832.8 | NP_000192.2 | |||
LIMASI | XR_007067137.1 | n.131-5804_131-5803delAG | intron_variant | |||||
LIMASI | XR_007067138.1 | n.131-5804_131-5803delAG | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ICAM1 | ENST00000264832.8 | c.67+1373_67+1374delCT | intron_variant | 1 | NM_000201.3 | ENSP00000264832.2 | ||||
ICAM1 | ENST00000423829.2 | c.67+1373_67+1374delCT | intron_variant | 2 | ENSP00000413124.2 | |||||
ICAM1 | ENST00000588645.1 | c.67+1373_67+1374delCT | intron_variant | 2 | ENSP00000465680.1 | |||||
LIMASI | ENST00000592893.1 | n.142-12170_142-12169delAG | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.358 AC: 44027AN: 123130Hom.: 7746 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.358 AC: 44042AN: 123164Hom.: 7750 Cov.: 0 AF XY: 0.357 AC XY: 20581AN XY: 57626
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3386
ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at