Genetic Variant NM_016946.6:c.*1817G>A (chr1-160997054-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016946.6(F11R):c.*1817G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,218 control chromosomes in the GnomAD database, including 4,545 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 ( 4539 hom., cov: 32)

Exomes 𝑓: 0.30 ( 6 hom. )

Consequence

F11R
NM_016946.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470

Publications

19 publications found

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]

F11R links:

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ACMG classification

Classification was made for transcript

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 = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016946.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
F11R	NM_016946.6	MANE Select	c.*1817G>A	3_prime_UTR	Exon 10 of 10	NP_058642.1
F11R	NM_001382727.1		c.*1817G>A	3_prime_UTR	Exon 10 of 10	NP_001369656.1
F11R	NM_001382730.1		c.*1817G>A	3_prime_UTR	Exon 10 of 10	NP_001369659.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11R	ENST00000368026.11	TSL:1 MANE Select	c.*1817G>A		3_prime_UTR	Exon 10 of 10	ENSP00000357005.5

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34075

AN:

151960

Hom.:

4535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.250

GnomAD4 exome

AF:

0.300

AC:

AN:

140

Hom.:

Cov.:

AF XY:

0.355

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.294

AC:

AN:

136

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.224

AC:

34079

AN:

152078

Hom.:

4539

Cov.:

AF XY:

0.224

AC XY:

16636

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.0770

AC:

3196

AN:

41532

American (AMR)

AF:

0.254

AC:

3881

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

1084

AN:

3470

East Asian (EAS)

AF:

0.187

AC:

969

AN:

5174

South Asian (SAS)

AF:

0.145

AC:

697

AN:

4814

European-Finnish (FIN)

AF:

0.350

AC:

3694

AN:

10566

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.289

AC:

19632

AN:

67942

Other (OTH)

AF:

0.247

AC:

520

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1332

2664

3995

5327

6659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.267

Hom.:

9252

Bravo

AF:

0.215

Asia WGS

AF:

0.139

AC:

490

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.4

(source)

DANN

Benign

0.66

PhyloP100

-0.047

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over