5-116026451-A-G

Position:

• chr5-116026451-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173800.5(LVRN):​c.*333A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 326,524 control chromosomes in the GnomAD database, including 48,771 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 0.56 (25300 hom., cov: 33)
  • Exomes 𝑓: 0.51 (23471 hom.)
• Consequence: LVRN NM_173800.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LVRN	NM_173800.5	c.*333A>G		3_prime_UTR_variant	20/20	ENST00000357872.9	NP_776161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9	c.*333A>G		3_prime_UTR_variant	20/20	1	NM_173800.5	ENSP00000350541	P1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85622 AN: 152002 Hom.: 25248 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.508 AC: 88592 AN: 174404 Hom.: 23471 Cov.: 2 AF XY: 0.512 AC XY: 48273 AN XY: 94322

Gnomad4 AFR exome AF: 0.740

Gnomad4 AMR exome AF: 0.599

Gnomad4 ASJ exome AF: 0.398

Gnomad4 EAS exome AF: 0.781

Gnomad4 SAS exome AF: 0.531

Gnomad4 FIN exome AF: 0.406

Gnomad4 NFE exome AF: 0.484

Gnomad4 OTH exome AF: 0.502

GnomAD4 genome AF: 0.564 AC: 85734 AN: 152120 Hom.: 25300 Cov.: 33 AF XY: 0.559 AC XY: 41586 AN XY: 74386

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.542

Alfa AF: 0.507 Hom.: 8255

Bravo AF: 0.588

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.65

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: rs1508886; hg19: chr5-115362148; COSMIC: COSV63496805; COSMIC: COSV63496805;