5-116013678-C-T

Position:

• chr5-116013678-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LVRN	NM_173800.5	c.2343-742C>T		intron_variant		ENST00000357872.9	NP_776161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9	c.2343-742C>T		intron_variant		1	NM_173800.5	ENSP00000350541.4

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

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.748

Alfa AF: 0.702 Hom.: 48833

Bravo AF: 0.768

Asia WGS AF: 0.915 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.8
DANN	Benign	0.79

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

LitVar

Other links and lift over

dbSNP: rs1529442; hg19: chr5-115349375;