dbSNP rs7712021: LVRN:p.Asn582Asn (chr5-116001165-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_173800.5(LVRN):c.1746T>C(p.Asn582Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,613,368 control chromosomes in the GnomAD database, including 85,042 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 0.32 ( 7998 hom., cov: 32)

Exomes 𝑓: 0.32 ( 77044 hom. )

Consequence

LVRN
NM_173800.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.73

Publications

16 publications found

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 was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP7

Synonymous conserved (PhyloP=1.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LVRN	NM_173800.5 link	c.1746T>C	p.Asn582Asn	synonymous_variant	Exon 10 of 20	ENST00000357872.9	NP_776161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9 link	c.1746T>C	p.Asn582Asn	synonymous_variant	Exon 10 of 20	1	NM_173800.5	ENSP00000350541.4

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48741

AN:

151878

Hom.:

7995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.312

GnomAD2 exomes

AF:

0.287

AC:

72106

AN:

250986

AF XY:

0.286

show subpopulations

Gnomad AFR exome

AF:

0.320

Gnomad AMR exome

AF:

0.193

Gnomad ASJ exome

AF:

0.304

Gnomad EAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.356

Gnomad NFE exome

AF:

0.342

Gnomad OTH exome

AF:

0.306

GnomAD4 exome

AF:

0.320

AC:

467878

AN:

1461372

Hom.:

77044

Cov.:

AF XY:

0.316

AC XY:

229594

AN XY:

726966

show subpopulations

African (AFR)

AF:

0.324

AC:

10836

AN:

33426

American (AMR)

AF:

0.203

AC:

9060

AN:

44598

Ashkenazi Jewish (ASJ)

AF:

0.300

AC:

7826

AN:

26122

East Asian (EAS)

AF:

0.247

AC:

9813

AN:

39688

South Asian (SAS)

AF:

0.153

AC:

13155

AN:

86170

European-Finnish (FIN)

AF:

0.351

AC:

18739

AN:

53414

Middle Eastern (MID)

AF:

0.297

AC:

1713

AN:

5766

European-Non Finnish (NFE)

AF:

0.340

AC:

377922

AN:

1111828

Other (OTH)

AF:

0.312

AC:

18814

AN:

60360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

17858

35717

53575

71434

89292

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11864

23728

35592

47456

59320

<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:

0.321

AC:

48768

AN:

151996

Hom.:

7998

Cov.:

AF XY:

0.317

AC XY:

23570

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.324

AC:

13438

AN:

41446

American (AMR)

AF:

0.265

AC:

4056

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.302

AC:

1045

AN:

3462

East Asian (EAS)

AF:

0.236

AC:

1219

AN:

5166

South Asian (SAS)

AF:

0.154

AC:

744

AN:

4818

European-Finnish (FIN)

AF:

0.360

AC:

3796

AN:

10546

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23546

AN:

67970

Other (OTH)

AF:

0.309

AC:

653

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1681

3362

5044

6725

8406

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.331

Hom.:

5333

Bravo

AF:

0.316

Asia WGS

AF:

0.217

AC:

757

AN:

3478

EpiCase

AF:

0.346

EpiControl

AF:

0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

4.3

(source)

DANN

Benign

0.65

PhyloP100

1.7

Mutation Taster

=97/3

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