2-140510004-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_018557.3(LRP1B):c.8322C>T(p.Cys2774=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0644 in 1,613,798 control chromosomes in the GnomAD database, including 4,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.059 ( 355 hom., cov: 32)
Exomes 𝑓: 0.065 ( 3647 hom. )
Consequence
LRP1B
NM_018557.3 synonymous
NM_018557.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0130
Genes affected
LRP1B (HGNC:6693): (LDL receptor related protein 1B) This gene encodes a member of the low density lipoprotein (LDL) receptor family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands. Disruption of this gene has been reported in several types of cancer. [provided by RefSeq, Jun 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 2-140510004-G-A is Benign according to our data. Variant chr2-140510004-G-A is described in ClinVar as [Benign]. Clinvar id is 3055616.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.013 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP1B | NM_018557.3 | c.8322C>T | p.Cys2774= | synonymous_variant | 52/91 | ENST00000389484.8 | |
LRP1B | XM_017004341.2 | c.7932C>T | p.Cys2644= | synonymous_variant | 52/91 | ||
LRP1B | XM_047444771.1 | c.8433C>T | p.Cys2811= | synonymous_variant | 52/77 | ||
LRP1B | XM_017004342.1 | c.3174C>T | p.Cys1058= | synonymous_variant | 23/62 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP1B | ENST00000389484.8 | c.8322C>T | p.Cys2774= | synonymous_variant | 52/91 | 1 | NM_018557.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0592 AC: 8997AN: 152082Hom.: 355 Cov.: 32
GnomAD3 genomes
AF:
AC:
8997
AN:
152082
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0570 AC: 14317AN: 251362Hom.: 568 AF XY: 0.0579 AC XY: 7869AN XY: 135874
GnomAD3 exomes
AF:
AC:
14317
AN:
251362
Hom.:
AF XY:
AC XY:
7869
AN XY:
135874
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0650 AC: 94952AN: 1461598Hom.: 3647 Cov.: 31 AF XY: 0.0652 AC XY: 47385AN XY: 727108
GnomAD4 exome
AF:
AC:
94952
AN:
1461598
Hom.:
Cov.:
31
AF XY:
AC XY:
47385
AN XY:
727108
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0591 AC: 8996AN: 152200Hom.: 355 Cov.: 32 AF XY: 0.0588 AC XY: 4373AN XY: 74422
GnomAD4 genome
AF:
AC:
8996
AN:
152200
Hom.:
Cov.:
32
AF XY:
AC XY:
4373
AN XY:
74422
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
56
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
LRP1B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 16, 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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at