Variant rs1131498 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.577T>C(p.Phe193Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,607,898 control chromosomes in the GnomAD database, including 51,524 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict 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 same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.21 ( 3854 hom., cov: 32)

Exomes 𝑓: 0.25 ( 47670 hom. )

Consequence

SELL
NM_000655.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.230

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:

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

FIRRM 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=0.0014271736).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELL	NM_000655.5 linkuse as main transcript	c.577T>C	p.Phe193Leu	missense_variant	4/9	ENST00000236147.6	NP_000646.3
SELL	NR_029467.2 linkuse as main transcript	n.546T>C		non_coding_transcript_exon_variant	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELL	ENST00000236147.6 linkuse as main transcript	c.577T>C	p.Phe193Leu	missense_variant	4/9	1	NM_000655.5	ENSP00000236147	P1	P14151-1

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32356

AN:

151898

Hom.:

3855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.00502

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.227

GnomAD3 exomes

AF:

0.206

AC:

50921

AN:

247268

Hom.:

6079

AF XY:

0.211

AC XY:

28323

AN XY:

134154

show subpopulations

Gnomad AFR exome

AF:

0.152

Gnomad AMR exome

AF:

0.129

Gnomad ASJ exome

AF:

0.270

Gnomad EAS exome

AF:

0.00549

Gnomad SAS exome

AF:

0.163

Gnomad FIN exome

AF:

0.212

Gnomad NFE exome

AF:

0.273

Gnomad OTH exome

AF:

0.223

GnomAD4 exome

AF:

0.249

AC:

361860

AN:

1455882

Hom.:

47670

Cov.:

AF XY:

0.247

AC XY:

179173

AN XY:

724332

show subpopulations

Gnomad4 AFR exome

AF:

0.150

Gnomad4 AMR exome

AF:

0.136

Gnomad4 ASJ exome

AF:

0.269

Gnomad4 EAS exome

AF:

0.00404

Gnomad4 SAS exome

AF:

0.164

Gnomad4 FIN exome

AF:

0.209

Gnomad4 NFE exome

AF:

0.273

Gnomad4 OTH exome

AF:

0.231

GnomAD4 genome

AF:

0.213

AC:

32343

AN:

152016

Hom.:

3854

Cov.:

AF XY:

0.207

AC XY:

15406

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.00522

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.225

Alfa

AF:

0.254

Hom.:

8877

Bravo

AF:

0.210

TwinsUK

AF:

0.275

AC:

1021

ALSPAC

AF:

0.265

AC:

1021

ESP6500AA

AF:

0.143

AC:

541

ESP6500EA

AF:

0.267

AC:

2204

ExAC

AF:

0.207

AC:

25050

Asia WGS

AF:

0.0600

AC:

207

AN:

3478

EpiCase

AF:

0.280

EpiControl

AF:

0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.59

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Uncertain

0.98

Eigen

Benign

-0.41

Eigen_PC

Benign

-0.33

FATHMM_MKL

Benign

0.19

LIST_S2

Benign

0.38

MetaRNN

Benign

0.0014

MetaSVM

Benign

-0.64

MutationTaster

Benign

1.0

PrimateAI

Benign

0.44

PROVEAN

Uncertain

-3.0

REVEL

Uncertain

0.29

Sift

Benign

0.38

Sift4G

Benign

0.37

Vest4

0.13

MPC

0.021

ClinPred

0.014

GERP RS

3.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over