chr5-115985427-G-A

Position:

• chr5-115985427-G-A

Variant summary

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

The NM_173800.5(LVRN):​c.978+718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,902 control chromosomes in the GnomAD database, including 14,145 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 0.43 (14145 hom., cov: 32)
• Consequence: LVRN NM_173800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LVRN	NM_173800.5	c.978+718G>A		intron_variant		ENST00000357872.9	NP_776161.3
LVRN	XM_047416913.1	c.285+718G>A		intron_variant			XP_047272869.1
LVRN	XM_047416914.1	c.189+718G>A		intron_variant			XP_047272870.1
LVRN	XM_047416915.1	c.189+718G>A		intron_variant			XP_047272871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9	c.978+718G>A		intron_variant		1	NM_173800.5	ENSP00000350541	P1
LVRN	ENST00000504467.5	c.978+718G>A		intron_variant, NMD_transcript_variant		1		ENSP00000423604

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64965 AN: 151784 Hom.: 14125 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.428 AC: 65025 AN: 151902 Hom.: 14145 Cov.: 32 AF XY: 0.426 AC XY: 31590 AN XY: 74230

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.453

Alfa AF: 0.458 Hom.: 18337

Bravo AF: 0.431

Asia WGS AF: 0.390 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.45

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: rs6864491; hg19: chr5-115321124;