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GeneBe

1-169593666-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_003005.4(SELP):c.2346G>A(p.Thr782=) 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 (★).

Frequency

Genomes: 𝑓 0.28 ( 7892 hom., cov: 32)
Exomes 𝑓: 0.19 ( 31683 hom. )

Consequence

SELP
NM_003005.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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 criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.886 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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/exons MANE UniProt
SELPNM_003005.4 linkuse as main transcriptc.2346G>A p.Thr782= synonymous_variant 14/17 ENST00000263686.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SELPENST00000263686.11 linkuse as main transcriptc.2346G>A p.Thr782= synonymous_variant 14/171 NM_003005.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.282
AC:
42902
AN:
151908
Hom.:
7872
Cov.:
32
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.:
31
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.283
AC:
42957
AN:
152024
Hom.:
7892
Cov.:
32
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: criteria provided, single submitter
LINK: link

Submissions by phenotype

SELP-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 21, 2019This 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.

Other links and lift over

dbSNP: rs6128; hg19: chr1-169562904; COSMIC: COSV55252508; COSMIC: COSV55252508; API