dbSNP rs3917419: SELE:c.530-61C>T (chr1-169730678-G-A) – 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.530-61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 976,674 control chromosomes in the GnomAD database, including 74,031 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 0.36 ( 9979 hom., cov: 30)

Exomes 𝑓: 0.38 ( 64052 hom. )

Consequence

SELE
NM_000450.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Publications

13 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:

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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELE	NM_000450.2 link	c.530-61C>T		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.530-61C>T		intron_variant	Intron 4 of 13	1	NM_000450.2	ENSP00000331736.7		P16581

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

53822

AN:

150668

Hom.:

9980

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.345

Gnomad FIN

AF:

0.347

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.412

Gnomad OTH

AF:

0.379

GnomAD4 exome

AF:

0.382

AC:

315338

AN:

825910

Hom.:

64052

AF XY:

0.384

AC XY:

155851

AN XY:

406096

show subpopulations

African (AFR)

AF:

0.267

AC:

4954

AN:

18574

American (AMR)

AF:

0.328

AC:

5518

AN:

16812

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

6202

AN:

14108

East Asian (EAS)

AF:

0.110

AC:

3190

AN:

29080

South Asian (SAS)

AF:

0.334

AC:

7481

AN:

22374

European-Finnish (FIN)

AF:

0.339

AC:

13529

AN:

39864

Middle Eastern (MID)

AF:

0.460

AC:

1849

AN:

4022

European-Non Finnish (NFE)

AF:

0.401

AC:

259199

AN:

645664

Other (OTH)

AF:

0.379

AC:

13416

AN:

35412

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

9188

18375

27563

36750

45938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7930

15860

23790

31720

39650

<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:

0.357

AC:

53828

AN:

150764

Hom.:

9979

Cov.:

AF XY:

0.353

AC XY:

26005

AN XY:

73576

show subpopulations

African (AFR)

AF:

0.283

AC:

11637

AN:

41150

American (AMR)

AF:

0.377

AC:

5714

AN:

15164

Ashkenazi Jewish (ASJ)

AF:

0.423

AC:

1462

AN:

3460

East Asian (EAS)

AF:

0.134

AC:

691

AN:

5154

South Asian (SAS)

AF:

0.346

AC:

1654

AN:

4786

European-Finnish (FIN)

AF:

0.347

AC:

3489

AN:

10044

Middle Eastern (MID)

AF:

0.493

AC:

143

AN:

290

European-Non Finnish (NFE)

AF:

0.413

AC:

27932

AN:

67706

Other (OTH)

AF:

0.375

AC:

788

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1725

3450

5176

6901

8626

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.394

Hom.:

37521

Bravo

AF:

0.353

Asia WGS

AF:

0.240

AC:

833

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.7

(source)

DANN

Benign

0.50

PhyloP100

0.082

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