Variant rs4987382 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.1105A>G(p.Asn369Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00943 in 1,377,586 control chromosomes in the GnomAD database, including 856 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 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 0.047 ( 535 hom., cov: 32)

Exomes 𝑓: 0.0047 ( 321 hom. )

Consequence

SELL
NM_000655.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.234

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=0.0012456179).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELL	NM_000655.5 linkuse as main transcript	c.1105A>G	p.Asn369Asp	missense_variant	9/9	ENST00000236147.6
SELL	NR_029467.2 linkuse as main transcript	n.1074A>G		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELL	ENST00000236147.6 linkuse as main transcript	c.1105A>G	p.Asn369Asp	missense_variant	9/9	1	NM_000655.5	P1	P14151-1
SELL	ENST00000650983.1 linkuse as main transcript	c.1144A>G	p.Asn382Asp	missense_variant	9/9				P14151-2
SELL	ENST00000497295.1 linkuse as main transcript	c.100A>G	p.Asn34Asp	missense_variant	3/3	5
FIRRM	ENST00000498289.5 linkuse as main transcript	n.851+7866T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0471

AC:

7168

AN:

152172

Hom.:

532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0186

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.000970

Gnomad OTH

AF:

0.0392

GnomAD3 exomes

AF:

0.0126

AC:

1700

AN:

135144

Hom.:

129

AF XY:

0.00911

AC XY:

675

AN XY:

74128

show subpopulations

Gnomad AFR exome

AF:

0.155

Gnomad AMR exome

AF:

0.00731

Gnomad ASJ exome

AF:

0.0221

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000243

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000926

Gnomad OTH exome

AF:

0.00680

GnomAD4 exome

AF:

0.00473

AC:

5800

AN:

1225296

Hom.:

321

Cov.:

AF XY:

0.00430

AC XY:

2584

AN XY:

601140

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.00849

Gnomad4 ASJ exome

AF:

0.0231

Gnomad4 EAS exome

AF:

0.0000316

Gnomad4 SAS exome

AF:

0.000232

Gnomad4 FIN exome

AF:

0.0000225

Gnomad4 NFE exome

AF:

0.000727

Gnomad4 OTH exome

AF:

0.0125

GnomAD4 genome

AF:

0.0472

AC:

7188

AN:

152290

Hom.:

535

Cov.:

AF XY:

0.0460

AC XY:

3422

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.0185

Gnomad4 ASJ

AF:

0.0228

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000970

Gnomad4 OTH

AF:

0.0388

Alfa

AF:

0.0128

Hom.:

198

Bravo

AF:

0.0530

TwinsUK

AF:

0.00162

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.161

AC:

582

ESP6500EA

AF:

0.00246

AC:

ExAC

AF:

0.0148

AC:

1781

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.052

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.81

Cadd

Benign

9.2

Dann

Benign

0.87

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.0019

LIST_S2

Benign

0.28

MetaRNN

Benign

0.0012

MetaSVM

Benign

-0.95

MutationTaster

Benign

1.0

PrimateAI

Benign

0.33

PROVEAN

Benign

0.72

REVEL

Benign

0.078

Sift

Benign

1.0

Sift4G

Benign

1.0

Vest4

0.013

MPC

0.019

ClinPred

0.0028

GERP RS

4.1

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