Variant rs2223286 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.1100+44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 1,547,900 control chromosomes in the GnomAD database, including 81,722 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.

Frequency

Genomes: 𝑓 0.37 ( 12204 hom., cov: 32)

Exomes 𝑓: 0.31 ( 69518 hom. )

Consequence

SELL
NM_000655.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.938

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELL	NM_000655.5 link	c.1100+44A>G		intron_variant		ENST00000236147.6	NP_000646.3	P14151-1
SELL	NR_029467.2 link	n.1069+44A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SELL	ENST00000236147.6 link	c.1100+44A>G	intron_variant	1	NM_000655.5	ENSP00000236147.5	P14151-1
SELL	ENST00000650983.1 link	c.1139+44A>G	intron_variant			ENSP00000498227.1	P14151-2
SELL	ENST00000497295.1 link	c.92+44A>G	intron_variant	5		ENSP00000498707.1	A0A494C0S7
C1orf112	ENST00000498289.5 link	n.851+12559T>C	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56428

AN:

151954

Hom.:

12194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.331

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.357

GnomAD3 exomes

AF:

0.293

AC:

47820

AN:

163314

Hom.:

7913

AF XY:

0.295

AC XY:

25431

AN XY:

86270

show subpopulations

Gnomad AFR exome

AF:

0.604

Gnomad AMR exome

AF:

0.190

Gnomad ASJ exome

AF:

0.321

Gnomad EAS exome

AF:

0.108

Gnomad SAS exome

AF:

0.342

Gnomad FIN exome

AF:

0.260

Gnomad NFE exome

AF:

0.310

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.308

AC:

429749

AN:

1395828

Hom.:

69518

Cov.:

AF XY:

0.309

AC XY:

212617

AN XY:

689110

show subpopulations

Gnomad4 AFR exome

AF:

0.605

Gnomad4 AMR exome

AF:

0.201

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.0863

Gnomad4 SAS exome

AF:

0.341

Gnomad4 FIN exome

AF:

0.257

Gnomad4 NFE exome

AF:

0.309

Gnomad4 OTH exome

AF:

0.311

GnomAD4 genome

AF:

0.371

AC:

56476

AN:

152072

Hom.:

12204

Cov.:

AF XY:

0.366

AC XY:

27231

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.593

Gnomad4 AMR

AF:

0.265

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.330

Gnomad4 FIN

AF:

0.258

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.314

Hom.:

15631

Bravo

AF:

0.380

Asia WGS

AF:

0.232

AC:

807

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.17

DANN

Benign

0.50

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