5-116017971-C-T

Variant names:

• chr5-116017971-C-T
• rs2662467
• NM_173800.5:c.2756+2206C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173800.5(LVRN):​c.2756+2206C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,062 control chromosomes in the GnomAD database, including 3,015 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 0.18 (3015 hom., cov: 32)
• Consequence: LVRN NM_173800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LVRN	NM_173800.5	c.2756+2206C>T		intron_variant	Intron 18 of 19	ENST00000357872.9	NP_776161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9	c.2756+2206C>T		intron_variant	Intron 18 of 19	1	NM_173800.5	ENSP00000350541.4

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26783 AN: 151944 Hom.: 3014 Cov.: 32

Gnomad AFR AF: 0.0501

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.176 AC: 26774 AN: 152062 Hom.: 3015 Cov.: 32 AF XY: 0.172 AC XY: 12765 AN XY: 74328

African (AFR) AF: 0.0500 AC: 2073 AN: 41492

American (AMR) AF: 0.173 AC: 2647 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3466

East Asian (EAS) AF: 0.0780 AC: 404 AN: 5180

South Asian (SAS) AF: 0.144 AC: 692 AN: 4820

European-Finnish (FIN) AF: 0.228 AC: 2412 AN: 10558

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17262 AN: 67968

Other (OTH) AF: 0.184 AC: 388 AN: 2110

Alfa AF: 0.210 Hom.: 484

Bravo AF: 0.167

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.77
PhyloP100		-0.44
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: rs2662467; hg19: chr5-115353668;