1-169594713-T-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003005.4(SELP):c.2266A>C(p.Thr756Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 1,613,462 control chromosomes in the GnomAD database, including 8,585 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.074 ( 574 hom., cov: 33)

Exomes 𝑓: 0.099 ( 8011 hom. )

Consequence

SELP
NM_003005.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:3

Conservation

PhyloP100: -0.741

Publications

135 publications found

Variant links:

Genes affected

SELP (HGNC:10721): (selectin P) This gene encodes a 140 kDa protein that is stored in the alpha-granules of platelets and Weibel-Palade bodies of endothelial cells. This protein redistributes to the plasma membrane during platelet activation and degranulation and mediates the interaction of activated endothelial cells or platelets with leukocytes. The membrane protein is a calcium-dependent receptor that binds to sialylated forms of Lewis blood group carbohydrate antigens on neutrophils and monocytes. Alternative splice variants may occur but are not well documented. [provided by RefSeq, Jul 2008]

SELP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0021575987).

BP6

Variant 1-169594713-T-G is Benign according to our data. Variant chr1-169594713-T-G is described in ClinVar as [Benign]. Clinvar id is 13527.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4 link	c.2266A>C	p.Thr756Pro	missense_variant	Exon 13 of 17	ENST00000263686.11	NP_002996.2	P16109Q6NUL9A0A024R8Y9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11 link	c.2266A>C	p.Thr756Pro	missense_variant	Exon 13 of 17	1	NM_003005.4	ENSP00000263686.5		P16109

Frequencies

GnomAD3 genomes

AF:

0.0738

AC:

11228

AN:

152150

Hom.:

571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0200

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0803

Gnomad ASJ

AF:

0.0622

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.0373

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0788

GnomAD2 exomes

AF:

0.0821

AC:

20598

AN:

250820

AF XY:

0.0818

show subpopulations

Gnomad AFR exome

AF:

0.0179

Gnomad AMR exome

AF:

0.0859

Gnomad ASJ exome

AF:

0.0641

Gnomad EAS exome

AF:

0.000326

Gnomad FIN exome

AF:

0.122

Gnomad NFE exome

AF:

0.110

Gnomad OTH exome

AF:

0.0806

GnomAD4 exome

AF:

0.0994

AC:

145263

AN:

1461194

Hom.:

8011

Cov.:

AF XY:

0.0974

AC XY:

70807

AN XY:

726882

show subpopulations

African (AFR)

AF:

0.0160

AC:

535

AN:

33442

American (AMR)

AF:

0.0866

AC:

3869

AN:

44660

Ashkenazi Jewish (ASJ)

AF:

0.0618

AC:

1612

AN:

26104

East Asian (EAS)

AF:

0.000101

AC:

AN:

39690

South Asian (SAS)

AF:

0.0390

AC:

3364

AN:

86194

European-Finnish (FIN)

AF:

0.122

AC:

6520

AN:

53398

Middle Eastern (MID)

AF:

0.0437

AC:

252

AN:

5760

European-Non Finnish (NFE)

AF:

0.111

AC:

123748

AN:

1111592

Other (OTH)

AF:

0.0888

AC:

5359

AN:

60354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

6561

13122

19684

26245

32806

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0738

AC:

11237

AN:

152268

Hom.:

574

Cov.:

AF XY:

0.0732

AC XY:

5452

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0200

AC:

830

AN:

41564

American (AMR)

AF:

0.0809

AC:

1237

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0622

AC:

216

AN:

3472

East Asian (EAS)

AF:

0.00193

AC:

AN:

5194

South Asian (SAS)

AF:

0.0375

AC:

181

AN:

4826

European-Finnish (FIN)

AF:

0.127

AC:

1352

AN:

10612

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7233

AN:

67984

Other (OTH)

AF:

0.0770

AC:

163

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

547

1094

1642

2189

2736

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0921

Hom.:

3420

Bravo

AF:

0.0700

TwinsUK

AF:

0.121

AC:

447

ALSPAC

AF:

0.120

AC:

463

ESP6500AA

AF:

0.0225

AC:

ESP6500EA

AF:

0.106

AC:

914

ExAC

AF:

0.0820

AC:

9951

Asia WGS

AF:

0.0190

AC:

AN:

3478

EpiCase

AF:

0.103

EpiControl

AF:

0.100

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SELP-related disorder

Benign:1

Nov 15, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

SELECTIN P POLYMORPHISM

Benign:1

Aug 01, 1998

OMIM

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.36

CADD

Benign

4.3

(source)

DANN

Benign

0.73

DEOGEN2

Benign

0.021

T;.;T;T;T

Eigen

Benign

-0.96

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.73

T;T;T;T;T

MetaRNN

Benign

0.0022

T;T;T;T;T

MetaSVM

Benign

-0.85

PhyloP100

-0.74

PrimateAI

Benign

0.30

PROVEAN

Benign

-1.4

N;N;N;.;N

REVEL

Benign

0.28

Sift

Benign

0.20

T;T;T;.;T

Sift4G

Benign

0.15

T;T;T;T;T

Vest4

0.29, 0.31, 0.32, 0.28

MPC

0.18

ClinPred

0.028

GERP RS

-3.9

gMVP

0.56

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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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1-169594713-T-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over