dbSNP rs1062826: ENSG00000270149:n.*1597C>G (chr1-160998215-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000289779.7(ENSG00000270149):n.*1597C>G 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 0.224 in 152,498 control chromosomes in the GnomAD database, including 4,548 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 ( 4540 hom., cov: 32)

Exomes 𝑓: 0.19 ( 8 hom. )

Consequence

ENSG00000270149
ENST00000289779.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

11 publications found

Variant links:

Genes affected

ENSG00000270149 (HGNC:):

ENSG00000270149 links:

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:

Genome browser will be placed here

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=-1.0).

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 link	c.*656C>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000368026.11	NP_058642.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000270149	ENST00000289779.7 link	n.*1597C>G	non_coding_transcript_exon_variant	Exon 13 of 13	2		ENSP00000289779.4	A0A0A0MQY5
F11R	ENST00000368026.11 link	c.*656C>G	3_prime_UTR_variant	Exon 10 of 10	1	NM_016946.6	ENSP00000357005.5	Q9Y624-1
ENSG00000270149	ENST00000289779.7 link	n.*1597C>G	3_prime_UTR_variant	Exon 13 of 13	2		ENSP00000289779.4	A0A0A0MQY5
F11R	ENST00000537746.1 link	c.*656C>G	downstream_gene_variant		2		ENSP00000440812.1	Q9Y624-2

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34078

AN:

151962

Hom.:

4536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.353

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.250

GnomAD4 exome

AF:

0.187

AC:

AN:

418

Hom.:

Cov.:

AF XY:

0.199

AC XY:

AN XY:

246

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.278

AC:

AN:

144

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.375

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.140

AC:

AN:

236

Other (OTH)

AF:

0.111

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

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:

34082

AN:

152080

Hom.:

4540

Cov.:

AF XY:

0.224

AC XY:

16640

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0769

AC:

3193

AN:

41500

American (AMR)

AF:

0.254

AC:

3879

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1085

AN:

3466

East Asian (EAS)

AF:

0.188

AC:

973

AN:

5188

South Asian (SAS)

AF:

0.144

AC:

697

AN:

4824

European-Finnish (FIN)

AF:

0.350

AC:

3694

AN:

10554

Middle Eastern (MID)

AF:

0.281

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.289

AC:

19636

AN:

67960

Other (OTH)

AF:

0.247

AC:

521

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1317

2634

3951

5268

6585

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.134

Hom.:

319

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

-1.0

CADD

Benign

0.15

(source)

DANN

Benign

0.36

PhyloP100

-1.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over