5-115996478-T-G

Position:

• chr5-115996478-T-G

Variant summary

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

The NM_173800.5(LVRN):​c.1374+2624T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,042 control chromosomes in the GnomAD database, including 17,134 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 0.47 (17134 hom., cov: 32)
• Consequence: LVRN NM_173800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LVRN	NM_173800.5	c.1374+2624T>G		intron_variant		ENST00000357872.9	NP_776161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9	c.1374+2624T>G		intron_variant		1	NM_173800.5	ENSP00000350541	P1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71661 AN: 151924 Hom.: 17130 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.472 AC: 71696 AN: 152042 Hom.: 17134 Cov.: 32 AF XY: 0.473 AC XY: 35170 AN XY: 74324

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.457

Alfa AF: 0.445 Hom.: 4700

Bravo AF: 0.460

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.80

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: rs885120; hg19: chr5-115332175;