ENST00000609271.1:c.-201-4863A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000609271.1(SELE):c.-201-4863A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,208 control chromosomes in the GnomAD database, including 1,508 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 0.14 ( 1508 hom., cov: 32)
Consequence
SELE
ENST00000609271.1 intron
ENST00000609271.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0710
Publications
2 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=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.135 AC: 20570AN: 152090Hom.: 1508 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
20570
AN:
152090
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: 0.135 AC: 20586AN: 152208Hom.: 1508 Cov.: 32 AF XY: 0.137 AC XY: 10186AN XY: 74422 show subpopulations
GnomAD4 genome
AF:
AC:
20586
AN:
152208
Hom.:
Cov.:
32
AF XY:
AC XY:
10186
AN XY:
74422
show subpopulations
African (AFR)
AF:
AC:
3789
AN:
41534
American (AMR)
AF:
AC:
2819
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
585
AN:
3470
East Asian (EAS)
AF:
AC:
672
AN:
5174
South Asian (SAS)
AF:
AC:
935
AN:
4820
European-Finnish (FIN)
AF:
AC:
1363
AN:
10602
Middle Eastern (MID)
AF:
AC:
67
AN:
294
European-Non Finnish (NFE)
AF:
AC:
9890
AN:
68002
Other (OTH)
AF:
AC:
305
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
911
1822
2734
3645
4556
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
236
472
708
944
1180
<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:
Asia WGS
AF:
AC:
606
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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