rs3917454
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000450.2(SELE):c.529+123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 626,050 control chromosomes in the GnomAD database, including 442 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 0.029 ( 106 hom., cov: 31)
Exomes 𝑓: 0.033 ( 336 hom. )
Consequence
SELE
NM_000450.2 intron
NM_000450.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
SELE (HGNC:10718): (selectin E) The protein encoded by this gene is found in cytokine-stimulated endothelial cells and is thought to be responsible for the accumulation of blood leukocytes at sites of inflammation by mediating the adhesion of cells to the vascular lining. It exhibits structural features such as the presence of lectin- and EGF-like domains followed by short consensus repeat (SCR) domains that contain 6 conserved cysteine residues. These proteins are part of the selectin family of cell adhesion molecules. Adhesion molecules participate in the interaction between leukocytes and the endothelium and appear to be involved in the pathogenesis of atherosclerosis. [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=-0.89).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0288 (4382/152200) while in subpopulation NFE AF= 0.0455 (3097/67996). AF 95% confidence interval is 0.0442. There are 106 homozygotes in gnomad4. There are 2043 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 106 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELE | NM_000450.2 | c.529+123C>T | intron_variant | ENST00000333360.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELE | ENST00000333360.12 | c.529+123C>T | intron_variant | 1 | NM_000450.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0288 AC: 4383AN: 152082Hom.: 106 Cov.: 31
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GnomAD4 exome AF: 0.0330 AC: 15646AN: 473850Hom.: 336 Cov.: 6 AF XY: 0.0322 AC XY: 8077AN XY: 250658
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GnomAD4 genome ? AF: 0.0288 AC: 4382AN: 152200Hom.: 106 Cov.: 31 AF XY: 0.0274 AC XY: 2043AN XY: 74432
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ClinVar
Not reported inComputational scores
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Name
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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