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GeneBe

1-161000299-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_016946.6(F11R):c.438G>A(p.Gly146=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00943 in 1,614,114 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0069 ( 4 hom., cov: 31)
Exomes 𝑓: 0.0097 ( 80 hom. )

Consequence

F11R
NM_016946.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.217
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-161000299-C-T is Benign according to our data. Variant chr1-161000299-C-T is described in ClinVar as [Benign]. Clinvar id is 774586.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.217 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
F11RNM_016946.6 linkuse as main transcriptc.438G>A p.Gly146= synonymous_variant 5/10 ENST00000368026.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
F11RENST00000368026.11 linkuse as main transcriptc.438G>A p.Gly146= synonymous_variant 5/101 NM_016946.6 P1Q9Y624-1
F11RENST00000537746.1 linkuse as main transcriptc.291G>A p.Gly97= synonymous_variant 4/92 Q9Y624-2
F11RENST00000472573.5 linkuse as main transcriptn.355G>A non_coding_transcript_exon_variant 3/42
F11RENST00000335772.3 linkuse as main transcript downstream_gene_variant 4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00688
AC:
1047
AN:
152158
Hom.:
4
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00169
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.00229
Gnomad ASJ
AF:
0.0135
Gnomad EAS
AF:
0.000384
Gnomad SAS
AF:
0.00228
Gnomad FIN
AF:
0.0170
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0100
Gnomad OTH
AF:
0.00479
GnomAD3 exomes
AF:
0.00698
AC:
1756
AN:
251456
Hom.:
13
AF XY:
0.00720
AC XY:
978
AN XY:
135896
show subpopulations
Gnomad AFR exome
AF:
0.00160
Gnomad AMR exome
AF:
0.00130
Gnomad ASJ exome
AF:
0.0118
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00245
Gnomad FIN exome
AF:
0.0189
Gnomad NFE exome
AF:
0.00918
Gnomad OTH exome
AF:
0.00603
GnomAD4 exome
AF:
0.00970
AC:
14176
AN:
1461838
Hom.:
80
Cov.:
34
AF XY:
0.00943
AC XY:
6857
AN XY:
727216
show subpopulations
Gnomad4 AFR exome
AF:
0.00146
Gnomad4 AMR exome
AF:
0.00141
Gnomad4 ASJ exome
AF:
0.0110
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00255
Gnomad4 FIN exome
AF:
0.0176
Gnomad4 NFE exome
AF:
0.0109
Gnomad4 OTH exome
AF:
0.00825
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00688
AC:
1047
AN:
152276
Hom.:
4
Cov.:
31
AF XY:
0.00697
AC XY:
519
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.00168
Gnomad4 AMR
AF:
0.00229
Gnomad4 ASJ
AF:
0.0135
Gnomad4 EAS
AF:
0.000385
Gnomad4 SAS
AF:
0.00228
Gnomad4 FIN
AF:
0.0170
Gnomad4 NFE
AF:
0.0100
Gnomad4 OTH
AF:
0.00474
Alfa
AF:
0.00939
Hom.:
11
Bravo
AF:
0.00576
Asia WGS
AF:
0.000866
AC:
4
AN:
3478
EpiCase
AF:
0.00992
EpiControl
AF:
0.00936

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
8.3
Dann
Benign
0.66
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs72712862; hg19: chr1-160970089; API