Variant rs2229569 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000655.5(SELL):c.637C>T(p.Pro213Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,551,396 control chromosomes in the GnomAD database, including 21,682 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.19 ( 2949 hom., cov: 32)

Exomes 𝑓: 0.16 ( 18733 hom. )

Consequence

SELL
NM_000655.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.28

Variant links:

Genes affected

SELL (HGNC:10720): (selectin L) This gene encodes a cell surface adhesion molecule that belongs to a family of adhesion/homing receptors. The encoded protein contains a C-type lectin-like domain, a calcium-binding epidermal growth factor-like domain, and two short complement-like repeats. The gene product is required for binding and subsequent rolling of leucocytes on endothelial cells, facilitating their migration into secondary lymphoid organs and inflammation sites. Single-nucleotide polymorphisms in this gene have been associated with various diseases including immunoglobulin A nephropathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2009]

SELL links:

C1orf112 (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

C1orf112 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015850961).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELL	NM_000655.5 link	c.637C>T	p.Pro213Ser	missense_variant	5/9	ENST00000236147.6	NP_000646.3	P14151-1
SELL	NR_029467.2 link	n.606C>T		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELL	ENST00000236147.6 link	c.637C>T	p.Pro213Ser	missense_variant	5/9	1	NM_000655.5	ENSP00000236147.5		P14151-1

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28514

AN:

151962

Hom.:

2937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.209

GnomAD3 exomes

AF:

0.206

AC:

32564

AN:

157854

Hom.:

3841

AF XY:

0.202

AC XY:

16773

AN XY:

83192

show subpopulations

Gnomad AFR exome

AF:

0.247

Gnomad AMR exome

AF:

0.329

Gnomad ASJ exome

AF:

0.157

Gnomad EAS exome

AF:

0.257

Gnomad SAS exome

AF:

0.243

Gnomad FIN exome

AF:

0.173

Gnomad NFE exome

AF:

0.145

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.155

AC:

217436

AN:

1399316

Hom.:

18733

Cov.:

AF XY:

0.157

AC XY:

108635

AN XY:

690218

show subpopulations

Gnomad4 AFR exome

AF:

0.249

Gnomad4 AMR exome

AF:

0.323

Gnomad4 ASJ exome

AF:

0.162

Gnomad4 EAS exome

AF:

0.254

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.180

Gnomad4 NFE exome

AF:

0.135

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.188

AC:

28571

AN:

152080

Hom.:

2949

Cov.:

AF XY:

0.190

AC XY:

14136

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.242

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.172

Gnomad4 NFE

AF:

0.137

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.152

Hom.:

3301

Bravo

AF:

0.199

TwinsUK

AF:

0.135

AC:

499

ALSPAC

AF:

0.143

AC:

550

ESP6500AA

AF:

0.218

AC:

809

ESP6500EA

AF:

0.133

AC:

1076

ExAC

AF:

0.125

AC:

10903

Asia WGS

AF:

0.251

AC:

873

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.47

CADD

Uncertain

DANN

Uncertain

1.0

Eigen

Uncertain

0.61

Eigen_PC

Uncertain

0.58

FATHMM_MKL

Uncertain

0.91

LIST_S2

Benign

0.71

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.71

PrimateAI

Benign

0.33

PROVEAN

Pathogenic

-7.5

REVEL

Benign

0.24

Sift

Benign

0.063

Sift4G

Benign

0.062

Vest4

0.040

MPC

0.079

ClinPred

0.029

GERP RS

5.3

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over