rs3181092
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 1-100739088-A-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,072 control chromosomes in the GnomAD database, including 23,535 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 0.53 ( 23535 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
VCAM1
NM_001078.4 downstream_gene
NM_001078.4 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.91
Genes affected
VCAM1 (HGNC:12663): (vascular cell adhesion molecule 1) This gene is a member of the Ig superfamily and encodes a cell surface sialoglycoprotein expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2010]
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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 (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCAM1 | NM_001078.4 | downstream_gene_variant | ENST00000294728.7 | ||||
VCAM1 | NM_001199834.2 | downstream_gene_variant | |||||
VCAM1 | NM_080682.3 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCAM1 | ENST00000294728.7 | downstream_gene_variant | 1 | NM_001078.4 | P1 | ||||
VCAM1 | ENST00000347652.6 | downstream_gene_variant | 1 | ||||||
VCAM1 | ENST00000370115.1 | downstream_gene_variant | 5 | ||||||
VCAM1 | ENST00000603679.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.530 AC: 80568AN: 151954Hom.: 23525 Cov.: 33
GnomAD3 genomes
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33
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.530 AC: 80603AN: 152072Hom.: 23535 Cov.: 33 AF XY: 0.528 AC XY: 39220AN XY: 74336
GnomAD4 genome
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33
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at