Variant chr5-116022440-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_173800.5(LVRN):c.2806G>A(p.Val936Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00528 in 1,558,512 control chromosomes in the GnomAD database, including 310 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.027 ( 178 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 132 hom. )

Consequence

LVRN
NM_173800.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.105

Variant links:

Genes affected

LVRN (HGNC:26904): (laeverin) Predicted to enable metalloaminopeptidase activity; peptide binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including peptide catabolic process; proteolysis; and regulation of blood pressure. Predicted to be integral component of membrane. Predicted to be active in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LVRN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016358495).

BP6

Variant 5-116022440-G-A is Benign according to our data. Variant chr5-116022440-G-A is described in ClinVar as [Benign]. Clinvar id is 778868.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LVRN	NM_173800.5 linkuse as main transcript	c.2806G>A	p.Val936Ile	missense_variant	19/20	ENST00000357872.9	NP_776161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9 linkuse as main transcript	c.2806G>A	p.Val936Ile	missense_variant	19/20	1	NM_173800.5	ENSP00000350541	P1	Q6Q4G3-1

Frequencies

GnomAD3 genomes

AF:

0.0265

AC:

4033

AN:

152116

Hom.:

175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0897

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00950

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0238

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000367

Gnomad OTH

AF:

0.0106

GnomAD3 exomes

AF:

0.00840

AC:

1885

AN:

224496

Hom.:

AF XY:

0.00685

AC XY:

836

AN XY:

122010

show subpopulations

Gnomad AFR exome

AF:

0.0892

Gnomad AMR exome

AF:

0.00446

Gnomad ASJ exome

AF:

0.000109

Gnomad EAS exome

AF:

0.0241

Gnomad SAS exome

AF:

0.000503

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000325

Gnomad OTH exome

AF:

0.00387

GnomAD4 exome

AF:

0.00298

AC:

4184

AN:

1406278

Hom.:

132

Cov.:

AF XY:

0.00267

AC XY:

1872

AN XY:

701426

show subpopulations

Gnomad4 AFR exome

AF:

0.0876

Gnomad4 AMR exome

AF:

0.00479

Gnomad4 ASJ exome

AF:

0.0000396

Gnomad4 EAS exome

AF:

0.0190

Gnomad4 SAS exome

AF:

0.000603

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000163

Gnomad4 OTH exome

AF:

0.00617

GnomAD4 genome

AF:

0.0266

AC:

4047

AN:

152234

Hom.:

178

Cov.:

AF XY:

0.0259

AC XY:

1925

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0897

Gnomad4 AMR

AF:

0.00943

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0241

Gnomad4 SAS

AF:

0.000828

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000368

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00577

Hom.:

Bravo

AF:

0.0296

ESP6500AA

AF:

0.0786

AC:

346

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.00989

AC:

1201

Asia WGS

AF:

0.0230

AC:

AN:

3478

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.062

DANN

Benign

0.22

DEOGEN2

Benign

0.00088

.;T

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00099

LIST_S2

Benign

0.39

T;T

MetaRNN

Benign

0.0016

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

-0.83

.;N

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.39

PROVEAN

Benign

0.47

.;N

REVEL

Benign

0.012

Sift

Benign

0.58

.;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0030

.;B

Vest4

0.029

MVP

0.088

MPC

0.062

ClinPred

0.00085

GERP RS

-6.4

Varity_R

0.035

gMVP

0.069

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over