ENST00000289779.7:n.*1378C>T

Variant names:

• chr1-160998434-G-A
• rs836
• ENST00000289779.7:n.*1378C>T

Variant summary

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

The ENST00000289779.7(ENSG00000270149):​n.*1378C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 219,578 control chromosomes in the GnomAD database, including 6,735 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 (4536 hom., cov: 32)
  • Exomes 𝑓: 0.24 (2199 hom.)
• Consequence: ENSG00000270149 ENST00000289779.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 17 publications found

Genes affected

ENSG00000270149 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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 rank	MANE	Protein	UniProt
F11R	NM_016946.6	c.*437C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000368026.11	NP_058642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270149	ENST00000289779.7	n.*1378C>T		non_coding_transcript_exon_variant	Exon 13 of 13	2		ENSP00000289779.4
F11R	ENST00000368026.11	c.*437C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_016946.6	ENSP00000357005.5
ENSG00000270149	ENST00000289779.7	n.*1378C>T		3_prime_UTR_variant	Exon 13 of 13	2		ENSP00000289779.4
F11R	ENST00000537746.1	c.*437C>T		3_prime_UTR_variant	Exon 9 of 9	2		ENSP00000440812.1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34093 AN: 151932 Hom.: 4532 Cov.: 32

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.249

GnomAD4 exome AF: 0.242 AC: 16319 AN: 67528 Hom.: 2199 Cov.: 0 AF XY: 0.235 AC XY: 8215 AN XY: 35028

African (AFR) AF: 0.0677 AC: 142 AN: 2096

American (AMR) AF: 0.263 AC: 1048 AN: 3990

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 476 AN: 1738

East Asian (EAS) AF: 0.176 AC: 670 AN: 3806

South Asian (SAS) AF: 0.124 AC: 919 AN: 7388

European-Finnish (FIN) AF: 0.315 AC: 892 AN: 2828

Middle Eastern (MID) AF: 0.223 AC: 59 AN: 264

European-Non Finnish (NFE) AF: 0.268 AC: 11189 AN: 41758

Other (OTH) AF: 0.252 AC: 924 AN: 3660

GnomAD4 genome AF: 0.224 AC: 34097 AN: 152050 Hom.: 4536 Cov.: 32 AF XY: 0.224 AC XY: 16626 AN XY: 74298

African (AFR) AF: 0.0777 AC: 3227 AN: 41514

American (AMR) AF: 0.254 AC: 3881 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1084 AN: 3470

East Asian (EAS) AF: 0.188 AC: 972 AN: 5176

South Asian (SAS) AF: 0.145 AC: 699 AN: 4818

European-Finnish (FIN) AF: 0.349 AC: 3676 AN: 10524

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19634 AN: 67952

Other (OTH) AF: 0.247 AC: 521 AN: 2112

Alfa AF: 0.188 Hom.: 629

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	-0.94
CADD	Benign	0.52
DANN	Benign	0.37
PhyloP100		-0.42
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs836; hg19: chr1-160968224;