Variant 1-169597088-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003005.4(SELP):c.1794C>T(p.Cys598=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,607,158 control chromosomes in the GnomAD database, including 22,084 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.23 ( 7157 hom., cov: 32)

Exomes 𝑓: 0.12 ( 14927 hom. )

Consequence

SELP
NM_003005.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0220

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=-0.73).

BP6

Variant 1-169597088-G-A is Benign according to our data. Variant chr1-169597088-G-A is described in ClinVar as [Benign]. Clinvar id is 3056728.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.022 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELP	NM_003005.4 linkuse as main transcript	c.1794C>T	p.Cys598=	synonymous_variant	11/17	ENST00000263686.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELP	ENST00000263686.11 linkuse as main transcript	c.1794C>T	p.Cys598=	synonymous_variant	11/17	1	NM_003005.4	P1

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34744

AN:

151986

Hom.:

7143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.556

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.0862

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0261

Gnomad FIN

AF:

0.0767

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.200

GnomAD3 exomes

AF:

0.113

AC:

27913

AN:

247452

Hom.:

3747

AF XY:

0.102

AC XY:

13685

AN XY:

133782

show subpopulations

Gnomad AFR exome

AF:

0.568

Gnomad AMR exome

AF:

0.0914

Gnomad ASJ exome

AF:

0.0861

Gnomad EAS exome

AF:

0.000653

Gnomad SAS exome

AF:

0.0231

Gnomad FIN exome

AF:

0.0771

Gnomad NFE exome

AF:

0.108

Gnomad OTH exome

AF:

0.109

GnomAD4 exome

AF:

0.117

AC:

170868

AN:

1455054

Hom.:

14927

Cov.:

AF XY:

0.113

AC XY:

81713

AN XY:

723814

show subpopulations

Gnomad4 AFR exome

AF:

0.571

Gnomad4 AMR exome

AF:

0.0986

Gnomad4 ASJ exome

AF:

0.0904

Gnomad4 EAS exome

AF:

0.000378

Gnomad4 SAS exome

AF:

0.0235

Gnomad4 FIN exome

AF:

0.0797

Gnomad4 NFE exome

AF:

0.118

Gnomad4 OTH exome

AF:

0.135

GnomAD4 genome

AF:

0.229

AC:

34804

AN:

152104

Hom.:

7157

Cov.:

AF XY:

0.220

AC XY:

16394

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.556

Gnomad4 AMR

AF:

0.143

Gnomad4 ASJ

AF:

0.0862

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.0259

Gnomad4 FIN

AF:

0.0767

Gnomad4 NFE

AF:

0.116

Gnomad4 OTH

AF:

0.201

Alfa

AF:

0.147

Hom.:

3313

Bravo

AF:

0.252

Asia WGS

AF:

0.0530

AC:

187

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SELP-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 06, 2019

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

-0.73

CADD

Benign

7.0

DANN

Benign

0.52

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