rs1062827

chr1-160997054-C-T

Variant summary

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

The NM_016946.6(F11R):c.*1817G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,218 control chromosomes in the GnomAD database, including 4,545 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 0.22 (4539 hom., cov: 32)
  • Exomes 𝑓: 0.30 (6 hom.)
• Consequence: F11R NM_016946.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F11R	NM_016946.6	c.*1817G>A		3_prime_UTR_variant	10/10	ENST00000368026.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F11R	ENST00000368026.11	c.*1817G>A		3_prime_UTR_variant	10/10	1	NM_016946.6	P1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34075 AN: 151960 Hom.: 4535 Cov.: 32

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.250

GnomAD4 exome AF: 0.300 AC: 42 AN: 140 Hom.: 6 Cov.: 0 AF XY: 0.355 AC XY: 27 AN XY: 76

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.294

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.224 AC: 34079 AN: 152078 Hom.: 4539 Cov.: 32 AF XY: 0.224 AC XY: 16636 AN XY: 74346

Gnomad4 AFR AF: 0.0770

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.247

Alfa AF: 0.274 Hom.: 7502

Bravo AF: 0.215

Asia WGS AF: 0.139 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.4
Dann	Benign	0.66

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: rs1062827; hg19: chr1-160966844;