Genetic Variant SELE:c.529+474A>G (chr1-169731361-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000450.2(SELE):c.529+474A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,966 control chromosomes in the GnomAD database, including 48,806 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 0.79 ( 48593 hom., cov: 31)

Exomes 𝑓: 0.71 ( 213 hom. )

Consequence

SELE
NM_000450.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Publications

18 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]

SELE links:

FIRRM (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

FIRRM links:

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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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELE	NM_000450.2 link	c.529+474A>G		intron_variant	Intron 4 of 13	ENST00000333360.12	NP_000441.2	P16581

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12 link	c.529+474A>G		intron_variant	Intron 4 of 13	1	NM_000450.2	ENSP00000331736.7		P16581

Frequencies

GnomAD3 genomes

AF:

0.793

AC:

120541

AN:

152026

Hom.:

48536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.949

Gnomad AMI

AF:

0.629

Gnomad AMR

AF:

0.791

Gnomad ASJ

AF:

0.806

Gnomad EAS

AF:

0.711

Gnomad SAS

AF:

0.821

Gnomad FIN

AF:

0.705

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.717

Gnomad OTH

AF:

0.799

GnomAD4 exome

AF:

0.714

AC:

587

AN:

822

Hom.:

213

AF XY:

0.728

AC XY:

271

AN XY:

372

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.830

AC:

AN:

100

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.773

AC:

AN:

European-Finnish (FIN)

AF:

0.600

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.692

AC:

450

AN:

650

Other (OTH)

AF:

0.824

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.793

AC:

120657

AN:

152144

Hom.:

48593

Cov.:

AF XY:

0.792

AC XY:

58884

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.949

AC:

39445

AN:

41544

American (AMR)

AF:

0.791

AC:

12083

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.806

AC:

2796

AN:

3470

East Asian (EAS)

AF:

0.711

AC:

3671

AN:

5160

South Asian (SAS)

AF:

0.822

AC:

3957

AN:

4816

European-Finnish (FIN)

AF:

0.705

AC:

7447

AN:

10562

Middle Eastern (MID)

AF:

0.925

AC:

272

AN:

294

European-Non Finnish (NFE)

AF:

0.717

AC:

48731

AN:

67998

Other (OTH)

AF:

0.797

AC:

1683

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1229

2457

3686

4914

6143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

858

1716

2574

3432

4290

<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:

0.740

Hom.:

55833

Bravo

AF:

0.806

Asia WGS

AF:

0.768

AC:

2668

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.82

(source)

DANN

Benign

0.32

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over