rs2278815

chr7-128241798-G-Achr7-128241798-G-C

Variant summary

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

The NM_000230.3(LEP):c.-29+492G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,100 control chromosomes in the GnomAD database, including 17,856 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 0.44 (17856 hom., cov: 33)
• Consequence: LEP NM_000230.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

Genes affected

LEP (HGNC:6553): (leptin) This gene encodes a protein that is secreted by white adipocytes into the circulation and plays a major role in the regulation of energy homeostasis. Circulating leptin binds to the leptin receptor in the brain, which activates downstream signaling pathways that inhibit feeding and promote energy expenditure. This protein also has several endocrine functions, and is involved in the regulation of immune and inflammatory responses, hematopoiesis, angiogenesis, reproduction, bone formation and wound healing. Mutations in this gene and its regulatory regions cause severe obesity and morbid obesity with hypogonadism in human patients. A mutation in this gene has also been linked to type 2 diabetes mellitus development. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LEP	NM_000230.3	c.-29+492G>A		intron_variant		ENST00000308868.5
LEP	XM_005250340.6	c.-29+492G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LEP	ENST00000308868.5	c.-29+492G>A		intron_variant		1	NM_000230.3	P1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67496 AN: 151982 Hom.: 17852 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.444 AC: 67514 AN: 152100 Hom.: 17856 Cov.: 33 AF XY: 0.452 AC XY: 33571 AN XY: 74338

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.476

Alfa AF: 0.533 Hom.: 21395

Bravo AF: 0.423

Asia WGS AF: 0.656 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.7
Dann	Benign	0.80

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: rs2278815; hg19: chr7-127881851;