5-116013678-C-T

Variant names:

• chr5-116013678-C-T
• rs1529442
• NM_173800.5:c.2343-742C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173800.5(LVRN):​c.2343-742C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,014 control chromosomes in the GnomAD database, including 43,458 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 0.75 (43458 hom., cov: 30)
• Consequence: LVRN NM_173800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173800.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LVRN	NM_173800.5	MANE Select	c.2343-742C>T		intron	N/A	NP_776161.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LVRN	ENST00000357872.9	TSL:1 MANE Select	c.2343-742C>T		intron	N/A	ENSP00000350541.4
	LVRN	ENST00000504467.5	TSL:1	n.*83-742C>T		intron	N/A	ENSP00000423604.1
	LVRN	ENST00000503329.5	TSL:2	n.*646-742C>T		intron	N/A	ENSP00000427418.1

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114126 AN: 151896 Hom.: 43403 Cov.: 30

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.744

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.752 AC: 114243 AN: 152014 Hom.: 43458 Cov.: 30 AF XY: 0.752 AC XY: 55897 AN XY: 74294

African (AFR) AF: 0.845 AC: 35062 AN: 41488

American (AMR) AF: 0.777 AC: 11860 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2447 AN: 3466

East Asian (EAS) AF: 0.956 AC: 4935 AN: 5160

South Asian (SAS) AF: 0.867 AC: 4173 AN: 4814

European-Finnish (FIN) AF: 0.612 AC: 6458 AN: 10550

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46708 AN: 67956

Other (OTH) AF: 0.748 AC: 1578 AN: 2110

Alfa AF: 0.709 Hom.: 63369

Bravo AF: 0.768

Asia WGS AF: 0.915 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.8
DANN	Benign	0.79
PhyloP100		0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1529442; hg19: chr5-115349375;