5-116026451-A-G

Variant names:

• chr5-116026451-A-G
• rs1508886
• NM_173800.5:c.*333A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 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.*333A>G		3_prime_UTR	Exon 20 of 20	NP_776161.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LVRN	ENST00000357872.9	TSL:1 MANE Select	c.*333A>G		3_prime_UTR	Exon 20 of 20	ENSP00000350541.4
	LVRN	ENST00000503329.5	TSL:2	n.*1650A>G		non_coding_transcript_exon	Exon 16 of 16	ENSP00000427418.1
	LVRN	ENST00000512413.1	TSL:2	n.1276A>G		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.740 AC: 3086 AN: 4172

American (AMR) AF: 0.599 AC: 3264 AN: 5448

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1837 AN: 4616

East Asian (EAS) AF: 0.781 AC: 5147 AN: 6592

South Asian (SAS) AF: 0.531 AC: 16061 AN: 30252

European-Finnish (FIN) AF: 0.406 AC: 3506 AN: 8626

Middle Eastern (MID) AF: 0.433 AC: 289 AN: 668

European-Non Finnish (NFE) AF: 0.484 AC: 50854 AN: 104970

Other (OTH) AF: 0.502 AC: 4548 AN: 9060

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

African (AFR) AF: 0.725 AC: 30075 AN: 41476

American (AMR) AF: 0.576 AC: 8802 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3470

East Asian (EAS) AF: 0.763 AC: 3958 AN: 5188

South Asian (SAS) AF: 0.551 AC: 2658 AN: 4826

European-Finnish (FIN) AF: 0.385 AC: 4068 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33073 AN: 67992

Other (OTH) AF: 0.542 AC: 1147 AN: 2116

Alfa AF: 0.513 Hom.: 13049

Bravo AF: 0.588

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.65
PhyloP100		3.4
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: rs1508886; hg19: chr5-115362148; COSMIC: COSV63496805; COSMIC: COSV63496805;