rs2481084

Variant names:

• chr1-161019824-T-C
• rs2481084
• NM_016946.6:c.64+1186A>G

Variant summary

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

The NM_016946.6(F11R):​c.64+1186A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,030 control chromosomes in the GnomAD database, including 4,705 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 0.24 (4705 hom., cov: 31)
• Consequence: F11R NM_016946.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 18 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F11R	NM_016946.6	c.64+1186A>G		intron_variant	Intron 1 of 9	ENST00000368026.11	NP_058642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F11R	ENST00000368026.11	c.64+1186A>G		intron_variant	Intron 1 of 9	1	NM_016946.6	ENSP00000357005.5
ENSG00000270149	ENST00000289779.7	n.*105+1186A>G		intron_variant	Intron 4 of 12	2		ENSP00000289779.4

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36959 AN: 151912 Hom.: 4701 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.243 AC: 36972 AN: 152030 Hom.: 4705 Cov.: 31 AF XY: 0.242 AC XY: 17986 AN XY: 74298

African (AFR) AF: 0.170 AC: 7066 AN: 41458

American (AMR) AF: 0.264 AC: 4033 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3468

East Asian (EAS) AF: 0.188 AC: 976 AN: 5178

South Asian (SAS) AF: 0.146 AC: 702 AN: 4820

European-Finnish (FIN) AF: 0.323 AC: 3415 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18749 AN: 67966

Other (OTH) AF: 0.268 AC: 566 AN: 2112

Alfa AF: 0.265 Hom.: 22974

Bravo AF: 0.241

Asia WGS AF: 0.145 AC: 509 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	10
DANN	Benign	0.81
PhyloP100		1.3
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: rs2481084; hg19: chr1-160989614;