rs7602

chr1-65432268-G-A

Variant summary

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

The NM_017526.5(LEPROT):c.*349G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,000,398 control chromosomes in the GnomAD database, including 26,715 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 0.26 (5639 hom., cov: 32)
  • Exomes 𝑓: 0.22 (21076 hom.)
• Consequence: LEPROT NM_017526.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

Genes affected

LEPROT (HGNC:29477): (leptin receptor overlapping transcript) LEPROT is associated with the Golgi complex and endosomes and has a role in cell surface expression of growth hormone receptor (GHR; MIM 600946) and leptin receptor (OBR, or LEPR; MIM 601007), thereby altering receptor-mediated cell signaling (Couturier et al., 2007 [PubMed 18042720]; Touvier et al., 2009 [PubMed 19907080]).[supplied by OMIM, Jul 2010]

LEPR (HGNC:6554): (leptin receptor) The protein encoded by this gene belongs to the gp130 family of cytokine receptors that are known to stimulate gene transcription via activation of cytosolic STAT proteins. This protein is a receptor for leptin (an adipocyte-specific hormone that regulates body weight), and is involved in the regulation of fat metabolism, as well as in a novel hematopoietic pathway that is required for normal lymphopoiesis. Mutations in this gene have been associated with obesity and pituitary dysfunction. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. It is noteworthy that this gene and LEPROT gene (GeneID:54741) share the same promoter and the first 2 exons, however, encode distinct proteins (PMID:9207021).[provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LEPROT	NM_017526.5	c.*349G>A		3_prime_UTR_variant	4/4	ENST00000371065.9
LEPR	NM_002303.6	c.-21+6890G>A		intron_variant		ENST00000349533.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LEPROT	ENST00000371065.9	c.*349G>A		3_prime_UTR_variant	4/4	1	NM_017526.5	P1
LEPR	ENST00000349533.11	c.-21+6890G>A		intron_variant		1	NM_002303.6	P4

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39288 AN: 151912 Hom.: 5631 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.235

GnomAD4 exome AF: 0.220 AC: 186898 AN: 848368 Hom.: 21076 Cov.: 31 AF XY: 0.221 AC XY: 86824 AN XY: 393232

Gnomad4 AFR exome AF: 0.405

Gnomad4 AMR exome AF: 0.276

Gnomad4 ASJ exome AF: 0.244

Gnomad4 EAS exome AF: 0.118

Gnomad4 SAS exome AF: 0.310

Gnomad4 FIN exome AF: 0.116

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.237

GnomAD4 genome AF: 0.259 AC: 39324 AN: 152030 Hom.: 5639 Cov.: 32 AF XY: 0.255 AC XY: 18951 AN XY: 74320

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.237

Alfa AF: 0.238 Hom.: 2351

Bravo AF: 0.274

Asia WGS AF: 0.219 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.0
Dann	Benign	0.78

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: rs7602; hg19: chr1-65897951;