chr1-160999795-C-T

Variant names:

• chr1-160999795-C-T
• rs790056
• NM_016946.6:c.695-48G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016946.6(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 NM_016946.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 20 publications found

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]

ENSG00000270149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
F11R	NM_016946.6	c.695-48G>A		intron_variant	Intron 6 of 9	ENST00000368026.11	NP_058642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F11R	ENST00000368026.11	c.695-48G>A		intron_variant	Intron 6 of 9	1	NM_016946.6	ENSP00000357005.5
ENSG00000270149	ENST00000289779.7	n.*736-48G>A		intron_variant	Intron 9 of 12	2		ENSP00000289779.4
F11R	ENST00000537746.1	c.548-48G>A		intron_variant	Intron 5 of 8	2		ENSP00000440812.1
F11R	ENST00000472573.5	n.*115G>A		downstream_gene_variant		2

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

GnomAD2 exomes AF: 0.810 AC: 203184 AN: 250818 AF XY: 0.807

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 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

African (AFR) AF: 0.915 AC: 30506 AN: 33340

American (AMR) AF: 0.814 AC: 36399 AN: 44704

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 21638 AN: 26098

East Asian (EAS) AF: 0.862 AC: 34189 AN: 39666

South Asian (SAS) AF: 0.802 AC: 69079 AN: 86128

European-Finnish (FIN) AF: 0.778 AC: 41575 AN: 53414

Middle Eastern (MID) AF: 0.815 AC: 4691 AN: 5758

European-Non Finnish (NFE) AF: 0.794 AC: 878266 AN: 1105646

Other (OTH) AF: 0.800 AC: 48139 AN: 60148

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

African (AFR) AF: 0.911 AC: 37813 AN: 41506

American (AMR) AF: 0.775 AC: 11836 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2910 AN: 3470

East Asian (EAS) AF: 0.853 AC: 4401 AN: 5162

South Asian (SAS) AF: 0.805 AC: 3869 AN: 4806

European-Finnish (FIN) AF: 0.785 AC: 8311 AN: 10588

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53697 AN: 67960

Other (OTH) AF: 0.826 AC: 1746 AN: 2114

Alfa AF: 0.811 Hom.: 17501

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
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs790056; hg19: chr1-160969585;