Variant chr5-115984673-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2

The NM_173800.5(LVRN):c.942C>T(p.Asp314Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 1,613,582 control chromosomes in the GnomAD database, including 244 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 0.012 ( 9 hom., cov: 32)

Exomes 𝑓: 0.017 ( 235 hom. )

Consequence

LVRN
NM_173800.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.311

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP7

Synonymous conserved (PhyloP=0.311 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0119 (1815/152248) while in subpopulation NFE AF= 0.0171 (1160/68004). AF 95% confidence interval is 0.0162. There are 9 homozygotes in gnomad4. There are 885 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LVRN	NM_173800.5 linkuse as main transcript	c.942C>T	p.Asp314Asp	synonymous_variant	3/20	ENST00000357872.9	NP_776161.3	Q6Q4G3-1Q0P5U8
LVRN	XM_047416913.1 linkuse as main transcript	c.249C>T	p.Asp83Asp	synonymous_variant	3/20		XP_047272869.1
LVRN	XM_047416914.1 linkuse as main transcript	c.153C>T	p.Asp51Asp	synonymous_variant	3/20		XP_047272870.1
LVRN	XM_047416915.1 linkuse as main transcript	c.153C>T	p.Asp51Asp	synonymous_variant	3/20		XP_047272871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9 linkuse as main transcript	c.942C>T	p.Asp314Asp	synonymous_variant	3/20	1	NM_173800.5	ENSP00000350541.4		Q6Q4G3-1
LVRN	ENST00000504467.5 linkuse as main transcript	n.942C>T		non_coding_transcript_exon_variant	3/20	1		ENSP00000423604.1		Q6Q4G3-2

Frequencies

GnomAD3 genomes

AF:

0.0119

AC:

1816

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0145

Gnomad FIN

AF:

0.0138

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0171

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.0140

AC:

3524

AN:

250924

Hom.:

AF XY:

0.0147

AC XY:

1989

AN XY:

135610

show subpopulations

Gnomad AFR exome

AF:

0.00302

Gnomad AMR exome

AF:

0.00659

Gnomad ASJ exome

AF:

0.0300

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0145

Gnomad FIN exome

AF:

0.0158

Gnomad NFE exome

AF:

0.0182

Gnomad OTH exome

AF:

0.0162

GnomAD4 exome

AF:

0.0165

AC:

24166

AN:

1461334

Hom.:

235

Cov.:

AF XY:

0.0166

AC XY:

12078

AN XY:

726962

show subpopulations

Gnomad4 AFR exome

AF:

0.00311

Gnomad4 AMR exome

AF:

0.00666

Gnomad4 ASJ exome

AF:

0.0308

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0136

Gnomad4 FIN exome

AF:

0.0166

Gnomad4 NFE exome

AF:

0.0178

Gnomad4 OTH exome

AF:

0.0166

GnomAD4 genome

AF:

0.0119

AC:

1815

AN:

152248

Hom.:

Cov.:

AF XY:

0.0119

AC XY:

885

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00361

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.0274

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0143

Gnomad4 FIN

AF:

0.0138

Gnomad4 NFE

AF:

0.0171

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.0169

Hom.:

Bravo

AF:

0.0109

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.0166

EpiControl

AF:

0.0208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

2.3

DANN

Benign

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over