1-161019824-T-C

Position:

• chr1-161019824-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F11R	NM_016946.6	c.64+1186A>G		intron_variant		ENST00000368026.11	NP_058642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F11R	ENST00000368026.11	c.64+1186A>G		intron_variant		1	NM_016946.6	ENSP00000357005	P1
F11R	ENST00000537746.1	c.64+1186A>G		intron_variant		2		ENSP00000440812
F11R	ENST00000335772.3	n.134+1186A>G		intron_variant, non_coding_transcript_variant		4
F11R	ENST00000602966.1	n.166+1186A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.268

Alfa AF: 0.269 Hom.: 11305

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

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: rs2481084; hg19: chr1-160989614;