1-160998434-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000289779.7(ENSG00000270149):​n.*1378C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 67818 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 35188

African (AFR) AF: 0.00 AC: 0 AN: 2096

American (AMR) AF: 0.00 AC: 0 AN: 4000

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1746

East Asian (EAS) AF: 0.00 AC: 0 AN: 3816

South Asian (SAS) AF: 0.00 AC: 0 AN: 7426

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2834

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 264

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 41968

Other (OTH) AF: 0.00 AC: 0 AN: 3668

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.36
PhyloP100		-0.42
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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;