rs10244329

Positions:

• chr7-128248636-A-T

Variant summary

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

The NM_000230.3(LEP):​c.-28-3355A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,082 control chromosomes in the GnomAD database, including 19,226 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 0.50 (19226 hom., cov: 33)
• Consequence: LEP NM_000230.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LEP	NM_000230.3	c.-28-3355A>T		intron_variant		ENST00000308868.5	NP_000221.1
LEP	XM_005250340.6	c.-28-3355A>T		intron_variant			XP_005250397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LEP	ENST00000308868.5	c.-28-3355A>T		intron_variant		1	NM_000230.3	ENSP00000312652.4

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75831 AN: 151964 Hom.: 19212 Cov.: 33

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.499 AC: 75893 AN: 152082 Hom.: 19226 Cov.: 33 AF XY: 0.494 AC XY: 36691 AN XY: 74338

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.522

Alfa AF: 0.510 Hom.: 2465

Bravo AF: 0.505

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.39

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: rs10244329; hg19: chr7-127888689;