rs6131

Positions:

• chr1-169611647-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003005.4(SELP):​c.992G>A​(p.Ser331Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,613,720 control chromosomes in the GnomAD database, including 30,311 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.22 (4153 hom., cov: 32)
  • Exomes 𝑓: 0.18 (26158 hom.)
• Consequence: SELP NM_003005.4 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.75

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=9.726286E-4).
• BP6: Variant 1-169611647-C-T is Benign according to our data. Variant chr1-169611647-C-T is described in ClinVar as [Benign]. Clinvar id is 3060479.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELP	NM_003005.4	c.992G>A	p.Ser331Asn	missense_variant	7/17	ENST00000263686.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELP	ENST00000263686.11	c.992G>A	p.Ser331Asn	missense_variant	7/17	1	NM_003005.4	P1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33723 AN: 151900 Hom.: 4136 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.220

GnomAD3 exomes AF: 0.198 AC: 49569 AN: 250832 Hom.: 5435 AF XY: 0.201 AC XY: 27189 AN XY: 135526

Gnomad AFR exome AF: 0.323

Gnomad AMR exome AF: 0.0932

Gnomad ASJ exome AF: 0.241

Gnomad EAS exome AF: 0.216

Gnomad SAS exome AF: 0.250

Gnomad FIN exome AF: 0.201

Gnomad NFE exome AF: 0.190

Gnomad OTH exome AF: 0.198

GnomAD4 exome AF: 0.184 AC: 268245 AN: 1461702 Hom.: 26158 Cov.: 35 AF XY: 0.186 AC XY: 135318 AN XY: 727152

Gnomad4 AFR exome AF: 0.320

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.240

Gnomad4 EAS exome AF: 0.189

Gnomad4 SAS exome AF: 0.246

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.175

Gnomad4 OTH exome AF: 0.198

GnomAD4 genome AF: 0.222 AC: 33769 AN: 152018 Hom.: 4153 Cov.: 32 AF XY: 0.220 AC XY: 16330 AN XY: 74324

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.221

Alfa AF: 0.193 Hom.: 7471

Bravo AF: 0.221

TwinsUK AF: 0.165 AC: 612

ALSPAC AF: 0.166 AC: 641

ESP6500AA AF: 0.303 AC: 1336

ESP6500EA AF: 0.188 AC: 1618

ExAC AF: 0.206 AC: 24965

Asia WGS AF: 0.240 AC: 835 AN: 3478

EpiCase AF: 0.185

EpiControl AF: 0.182

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

SELP-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 28, 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
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.69	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.064
DANN	Benign	0.50
DEOGEN2	Benign	0.014	T;.;T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0055	N
LIST_S2	Benign	0.0022	T;T;T
MetaRNN	Benign	0.00097	T;T;T
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	1.0	P;P;P;P;P;P;P;P;P;P
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-0.66	N;N;N
REVEL	Benign	0.011
Sift	Benign	0.49	T;T;T
Sift4G	Benign	0.46	T;T;T
Vest4		0.048, 0.054
MPC		0.055
ClinPred		0.00086	T
GERP RS		-4.5
gMVP		0.086

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

Other links and lift over

dbSNP: rs6131; hg19: chr1-169580885; COSMIC: COSV55249092;