rs17482536

Variant names:

• chr5-115984673-C-G
• NM_173800.5:c.942C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-115984673-C-G
• chr5-115984673-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_173800.5(LVRN):​c.942C>G​(p.Asp314Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,350 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: LVRN NM_173800.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LVRN	NM_173800.5	c.942C>G	p.Asp314Glu	missense_variant	Exon 3 of 20	ENST00000357872.9	NP_776161.3
LVRN	XM_047416913.1	c.249C>G	p.Asp83Glu	missense_variant	Exon 3 of 20		XP_047272869.1
LVRN	XM_047416914.1	c.153C>G	p.Asp51Glu	missense_variant	Exon 3 of 20		XP_047272870.1
LVRN	XM_047416915.1	c.153C>G	p.Asp51Glu	missense_variant	Exon 3 of 20		XP_047272871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LVRN	ENST00000357872.9	c.942C>G	p.Asp314Glu	missense_variant	Exon 3 of 20	1	NM_173800.5	ENSP00000350541.4
LVRN	ENST00000504467.5	n.942C>G		non_coding_transcript_exon_variant	Exon 3 of 20	1		ENSP00000423604.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461350 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 726968

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	22
DANN	Benign	0.82
DEOGEN2	Benign	0.017	.;T
Eigen	Benign	0.14
Eigen_PC	Benign	0.10
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.55	T;T
M_CAP	Benign	0.013	T
MetaRNN	Benign	0.31	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.9	.;L
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-0.75	.;N
REVEL	Benign	0.19
Sift	Benign	1.0	.;T
Sift4G	Benign	0.67	T;T
Polyphen		1.0	.;D
Vest4		0.21
MutPred		0.69		.;Gain of sheet (P = 0.1208);
MVP		0.49
MPC		0.41
ClinPred		0.80	D
GERP RS		4.0
Varity_R		0.14
gMVP		0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.54		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.54		Position offset: -5
DS_DL_spliceai		0.52		Position offset: 36

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-115320370;