Genetic Variant SELP:p.Thr782Thr (chr1-169593666-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_003005.4(SELP):c.2346G>A(p.Thr782Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,612,630 control chromosomes in the GnomAD database, including 39,575 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.28 ( 7892 hom., cov: 32)

Exomes 𝑓: 0.19 ( 31683 hom. )

Consequence

SELP
NM_003005.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.886

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 1-169593666-C-T is Benign according to our data. Variant chr1-169593666-C-T is described in ClinVar as [Benign]. Clinvar id is 3059830.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.886 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4 link	c.2346G>A	p.Thr782Thr	synonymous_variant	Exon 14 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.2346G>A	p.Thr782Thr	synonymous_variant	Exon 14 of 17	1	NM_003005.4	ENSP00000263686.5		P16109

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42902

AN:

151908

Hom.:

7872

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.650

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.266

GnomAD3 exomes

AF:

0.241

AC:

60380

AN:

250966

Hom.:

10178

AF XY:

0.229

AC XY:

31038

AN XY:

135650

show subpopulations

Gnomad AFR exome

AF:

0.488

Gnomad AMR exome

AF:

0.255

Gnomad ASJ exome

AF:

0.196

Gnomad EAS exome

AF:

0.678

Gnomad SAS exome

AF:

0.167

Gnomad FIN exome

AF:

0.227

Gnomad NFE exome

AF:

0.158

Gnomad OTH exome

AF:

0.215

GnomAD4 exome

AF:

0.185

AC:

270454

AN:

1460606

Hom.:

31683

Cov.:

AF XY:

0.183

AC XY:

132978

AN XY:

726638

show subpopulations

Gnomad4 AFR exome

AF:

0.490

Gnomad4 AMR exome

AF:

0.259

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.594

Gnomad4 SAS exome

AF:

0.164

Gnomad4 FIN exome

AF:

0.228

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.227

GnomAD4 genome

AF:

0.283

AC:

42957

AN:

152024

Hom.:

7892

Cov.:

AF XY:

0.285

AC XY:

21207

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.482

Gnomad4 AMR

AF:

0.270

Gnomad4 ASJ

AF:

0.190

Gnomad4 EAS

AF:

0.649

Gnomad4 SAS

AF:

0.184

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.159

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.188

Hom.:

3863

Bravo

AF:

0.299

Asia WGS

AF:

0.442

AC:

1535

AN:

3478

EpiCase

AF:

0.157

EpiControl

AF:

0.159

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SELP-related disorder

Benign:1

Oct 21, 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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.69

DANN

Benign

0.37

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over