1-169724709-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000450.2(SELE):c.*16-200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0314 in 152,230 control chromosomes in the GnomAD database, including 112 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 0.031 ( 112 hom., cov: 32)
Consequence
SELE
NM_000450.2 intron
NM_000450.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.707
Publications
5 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0314 (4786/152230) while in subpopulation NFE AF = 0.0488 (3316/68018). AF 95% confidence interval is 0.0474. There are 112 homozygotes in GnomAd4. There are 2201 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 112 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0315 AC: 4788AN: 152112Hom.: 112 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
4788
AN:
152112
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0314 AC: 4786AN: 152230Hom.: 112 Cov.: 32 AF XY: 0.0296 AC XY: 2201AN XY: 74418 show subpopulations
GnomAD4 genome
AF:
AC:
4786
AN:
152230
Hom.:
Cov.:
32
AF XY:
AC XY:
2201
AN XY:
74418
show subpopulations
African (AFR)
AF:
AC:
383
AN:
41546
American (AMR)
AF:
AC:
555
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
196
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5182
South Asian (SAS)
AF:
AC:
38
AN:
4826
European-Finnish (FIN)
AF:
AC:
182
AN:
10582
Middle Eastern (MID)
AF:
AC:
12
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3316
AN:
68018
Other (OTH)
AF:
AC:
69
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
242
485
727
970
1212
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
52
104
156
208
260
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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