rs145651189
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_002303.6(LEPR):c.3019A>T(p.Ser1007Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000766 in 1,614,120 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002303.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000539 AC: 82AN: 152202Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00160 AC: 401AN: 250532Hom.: 8 AF XY: 0.00207 AC XY: 281AN XY: 135428
GnomAD4 exome AF: 0.000789 AC: 1154AN: 1461800Hom.: 15 Cov.: 30 AF XY: 0.00104 AC XY: 756AN XY: 727190
GnomAD4 genome AF: 0.000538 AC: 82AN: 152320Hom.: 2 Cov.: 32 AF XY: 0.000792 AC XY: 59AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:3
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See Variant Classification Assertion Criteria. -
Monogenic Non-Syndromic Obesity Uncertain:1
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Obesity due to leptin receptor gene deficiency Uncertain:1
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not specified Benign:1
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Monogenic diabetes Benign:1
ACMG Criteria:PP3 (3 predictors), BP4 (7 predictors), BS2 (4 homozygotes in South Asian in ExAC, 35 cases and 40 controls in type2diabetesgenetics.org), BP5 (found in case with GCK pathogenic variant) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at