chr2-140314950-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_018557.3(LRP1B):āc.12790G>Cā(p.Val4264Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 1,603,762 control chromosomes in the GnomAD database, including 308 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V4264I) has been classified as Likely benign.
Frequency
Consequence
NM_018557.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP1B | NM_018557.3 | c.12790G>C | p.Val4264Leu | missense_variant | 83/91 | ENST00000389484.8 | |
LRP1B | XM_017004341.2 | c.12400G>C | p.Val4134Leu | missense_variant | 83/91 | ||
LRP1B | XM_017004342.1 | c.7642G>C | p.Val2548Leu | missense_variant | 54/62 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP1B | ENST00000389484.8 | c.12790G>C | p.Val4264Leu | missense_variant | 83/91 | 1 | NM_018557.3 | P1 | |
LRP1B | ENST00000437977.5 | c.1486G>C | p.Val496Leu | missense_variant | 10/17 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0204 AC: 3095AN: 152024Hom.: 39 Cov.: 32
GnomAD3 exomes AF: 0.0157 AC: 3849AN: 245518Hom.: 44 AF XY: 0.0155 AC XY: 2061AN XY: 132728
GnomAD4 exome AF: 0.0165 AC: 23882AN: 1451620Hom.: 269 Cov.: 30 AF XY: 0.0164 AC XY: 11863AN XY: 721800
GnomAD4 genome AF: 0.0204 AC: 3100AN: 152142Hom.: 39 Cov.: 32 AF XY: 0.0202 AC XY: 1505AN XY: 74356
ClinVar
Submissions by phenotype
LRP1B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 23, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at