rs790056

Positions:

• chr1-160999795-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000368026.11(F11R):​c.695-48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 1,606,982 control chromosomes in the GnomAD database, including 518,873 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 0.83 (52156 hom., cov: 30)
  • Exomes 𝑓: 0.80 (466717 hom.)
• Consequence: F11R ENST00000368026.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

F11R (HGNC:14685): (F11 receptor) Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. The protein encoded by this immunoglobulin superfamily gene member is an important regulator of tight junction assembly in epithelia. In addition, the encoded protein can act as (1) a receptor for reovirus, (2) a ligand for the integrin LFA1, involved in leukocyte transmigration, and (3) a platelet receptor. Multiple 5' alternatively spliced variants, encoding the same protein, have been identified but their biological validity has not been established. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F11R	NM_016946.6	c.695-48G>A		intron_variant		ENST00000368026.11	NP_058642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F11R	ENST00000368026.11	c.695-48G>A		intron_variant		1	NM_016946.6	ENSP00000357005	P1
F11R	ENST00000537746.1	c.548-48G>A		intron_variant		2		ENSP00000440812

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125454 AN: 151962 Hom.: 52109 Cov.: 30

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.824

GnomAD3 exomes AF: 0.810 AC: 203184 AN: 250818 Hom.: 82532 AF XY: 0.807 AC XY: 109451 AN XY: 135550

Gnomad AFR exome AF: 0.914

Gnomad AMR exome AF: 0.817

Gnomad ASJ exome AF: 0.826

Gnomad EAS exome AF: 0.856

Gnomad SAS exome AF: 0.802

Gnomad FIN exome AF: 0.783

Gnomad NFE exome AF: 0.793

Gnomad OTH exome AF: 0.790

GnomAD4 exome AF: 0.800 AC: 1164482 AN: 1454902 Hom.: 466717 Cov.: 30 AF XY: 0.801 AC XY: 579797 AN XY: 724204

Gnomad4 AFR exome AF: 0.915

Gnomad4 AMR exome AF: 0.814

Gnomad4 ASJ exome AF: 0.829

Gnomad4 EAS exome AF: 0.862

Gnomad4 SAS exome AF: 0.802

Gnomad4 FIN exome AF: 0.778

Gnomad4 NFE exome AF: 0.794

Gnomad4 OTH exome AF: 0.800

GnomAD4 genome AF: 0.826 AC: 125557 AN: 152080 Hom.: 52156 Cov.: 30 AF XY: 0.823 AC XY: 61191 AN XY: 74320

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.826

Alfa AF: 0.813 Hom.: 10374

Bravo AF: 0.833

Asia WGS AF: 0.783 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.011
DANN	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs790056; hg19: chr1-160969585;