rs3917406

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000450.2(SELE):​c.38-139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 850,294 control chromosomes in the GnomAD database, including 35,064 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7403 hom., cov: 32)
Exomes 𝑓: 0.27 ( 27661 hom. )

Consequence

SELE
NM_000450.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.35
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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 1-169733137-A-G is Benign according to our data. Variant chr1-169733137-A-G is described in ClinVar as [Benign]. Clinvar id is 1684529.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SELENM_000450.2 linkuse as main transcriptc.38-139T>C intron_variant ENST00000333360.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SELEENST00000333360.12 linkuse as main transcriptc.38-139T>C intron_variant 1 NM_000450.2 P1

Frequencies

GnomAD3 genomes
AF:
0.303
AC:
45997
AN:
152006
Hom.:
7390
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.347
Gnomad AMI
AF:
0.239
Gnomad AMR
AF:
0.355
Gnomad ASJ
AF:
0.334
Gnomad EAS
AF:
0.496
Gnomad SAS
AF:
0.348
Gnomad FIN
AF:
0.303
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.328
GnomAD4 exome
AF:
0.267
AC:
186101
AN:
698170
Hom.:
27661
AF XY:
0.269
AC XY:
95482
AN XY:
354490
show subpopulations
Gnomad4 AFR exome
AF:
0.349
Gnomad4 AMR exome
AF:
0.403
Gnomad4 ASJ exome
AF:
0.321
Gnomad4 EAS exome
AF:
0.535
Gnomad4 SAS exome
AF:
0.346
Gnomad4 FIN exome
AF:
0.315
Gnomad4 NFE exome
AF:
0.230
Gnomad4 OTH exome
AF:
0.290
GnomAD4 genome
AF:
0.303
AC:
46057
AN:
152124
Hom.:
7403
Cov.:
32
AF XY:
0.307
AC XY:
22819
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.347
Gnomad4 AMR
AF:
0.355
Gnomad4 ASJ
AF:
0.334
Gnomad4 EAS
AF:
0.497
Gnomad4 SAS
AF:
0.349
Gnomad4 FIN
AF:
0.303
Gnomad4 NFE
AF:
0.244
Gnomad4 OTH
AF:
0.330
Alfa
AF:
0.274
Hom.:
906
Bravo
AF:
0.313
Asia WGS
AF:
0.395
AC:
1374
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Coronary artery disorder Benign:1
Benign, criteria provided, single submitterclinical testingRasad Genetic Department, Rasad Pathobiology and Genetic LaboratoryMay 12, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.43
DANN
Benign
0.31

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3917406; hg19: chr1-169702278; API