rs5030390
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000201.3(ICAM1):c.67+635G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,022 control chromosomes in the GnomAD database, including 261 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 0.051 ( 261 hom., cov: 32)
Consequence
ICAM1
NM_000201.3 intron
NM_000201.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.423
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0753 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ICAM1 | NM_000201.3 | c.67+635G>A | intron_variant | ENST00000264832.8 | |||
LIMASI | XR_007067138.1 | n.131-5067C>T | intron_variant, non_coding_transcript_variant | ||||
LIMASI | XR_007067137.1 | n.131-5067C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ICAM1 | ENST00000264832.8 | c.67+635G>A | intron_variant | 1 | NM_000201.3 | P1 | |||
LIMASI | ENST00000592893.1 | n.142-11433C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
ICAM1 | ENST00000423829.2 | c.67+635G>A | intron_variant | 2 | |||||
ICAM1 | ENST00000588645.1 | c.67+635G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0510 AC: 7745AN: 151904Hom.: 261 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0509 AC: 7739AN: 152022Hom.: 261 Cov.: 32 AF XY: 0.0490 AC XY: 3642AN XY: 74282
GnomAD4 genome
?
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32
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3642
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74282
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53
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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