2-169362361-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_004525.3(LRP2):c.39C>T(p.Leu13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000355 in 1,571,022 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L13L) has been classified as Likely benign.
Frequency
Consequence
NM_004525.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP2 | NM_004525.3 | c.39C>T | p.Leu13= | synonymous_variant | 1/79 | ENST00000649046.1 | |
LRP2 | XM_011511183.4 | c.39C>T | p.Leu13= | synonymous_variant | 1/78 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP2 | ENST00000649046.1 | c.39C>T | p.Leu13= | synonymous_variant | 1/79 | NM_004525.3 | P1 | ||
LRP2 | ENST00000443831.1 | c.39C>T | p.Leu13= | synonymous_variant | 1/23 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000998 AC: 171AN: 171400Hom.: 1 AF XY: 0.00131 AC XY: 123AN XY: 93806
GnomAD4 exome AF: 0.000371 AC: 526AN: 1418738Hom.: 2 Cov.: 33 AF XY: 0.000535 AC XY: 376AN XY: 702228
GnomAD4 genome AF: 0.000204 AC: 31AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 11, 2014 | - - |
LRP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 16, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Donnai-Barrow syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at