5-115986122-T-G

Variant names:

• chr5-115986122-T-G
• rs1366200
• NM_173800.5:c.978+1413T>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.978+1413T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,148 control chromosomes in the GnomAD database, including 14,558 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 0.41 (14558 hom., cov: 34)
• Consequence: LVRN NM_173800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 8 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LVRN	NM_173800.5	c.978+1413T>G		intron_variant	Intron 3 of 19	ENST00000357872.9	NP_776161.3
LVRN	XM_047416913.1	c.285+1413T>G		intron_variant	Intron 3 of 19		XP_047272869.1
LVRN	XM_047416914.1	c.189+1413T>G		intron_variant	Intron 3 of 19		XP_047272870.1
LVRN	XM_047416915.1	c.189+1413T>G		intron_variant	Intron 3 of 19		XP_047272871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9	c.978+1413T>G		intron_variant	Intron 3 of 19	1	NM_173800.5	ENSP00000350541.4
LVRN	ENST00000504467.5	n.978+1413T>G		intron_variant	Intron 3 of 19	1		ENSP00000423604.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62803 AN: 152030 Hom.: 14535 Cov.: 34

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.413 AC: 62868 AN: 152148 Hom.: 14558 Cov.: 34 AF XY: 0.418 AC XY: 31116 AN XY: 74390

African (AFR) AF: 0.521 AC: 21618 AN: 41488

American (AMR) AF: 0.493 AC: 7539 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1366 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4598 AN: 5182

South Asian (SAS) AF: 0.558 AC: 2688 AN: 4820

European-Finnish (FIN) AF: 0.245 AC: 2599 AN: 10600

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21263 AN: 67992

Other (OTH) AF: 0.430 AC: 908 AN: 2110

Alfa AF: 0.364 Hom.: 20963

Bravo AF: 0.434

Asia WGS AF: 0.712 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.57
PhyloP100		-2.2
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: rs1366200; hg19: chr5-115321819;