1-169724709-G-A

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.707

Publications

5 publications found
Variant links:
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]
FIRRM (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SELENM_000450.2 linkc.*16-200C>T intron_variant Intron 13 of 13 ENST00000333360.12 NP_000441.2 P16581

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SELEENST00000333360.12 linkc.*16-200C>T intron_variant Intron 13 of 13 1 NM_000450.2 ENSP00000331736.7 P16581

Frequencies

GnomAD3 genomes
AF:
0.0315
AC:
4788
AN:
152112
Hom.:
112
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00925
Gnomad AMI
AF:
0.0385
Gnomad AMR
AF:
0.0364
Gnomad ASJ
AF:
0.0565
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00787
Gnomad FIN
AF:
0.0172
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0488
Gnomad OTH
AF:
0.0330
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0314
AC:
4786
AN:
152230
Hom.:
112
Cov.:
32
AF XY:
0.0296
AC XY:
2201
AN XY:
74418
show subpopulations
African (AFR)
AF:
0.00922
AC:
383
AN:
41546
American (AMR)
AF:
0.0363
AC:
555
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.0565
AC:
196
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5182
South Asian (SAS)
AF:
0.00787
AC:
38
AN:
4826
European-Finnish (FIN)
AF:
0.0172
AC:
182
AN:
10582
Middle Eastern (MID)
AF:
0.0408
AC:
12
AN:
294
European-Non Finnish (NFE)
AF:
0.0488
AC:
3316
AN:
68018
Other (OTH)
AF:
0.0327
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:
0.0297
Hom.:
42
Bravo
AF:
0.0332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.44
DANN
Benign
0.22
PhyloP100
-0.71
Mutation Taster
=100/0
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs3917438; hg19: chr1-169693850; API