chr2-141120932-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018557.3(LRP1B):c.1014-58659G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,814 control chromosomes in the GnomAD database, including 6,792 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 0.29 ( 6792 hom., cov: 32)
Consequence
LRP1B
NM_018557.3 intron
NM_018557.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.282
Publications
4 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRP1B | NM_018557.3 | c.1014-58659G>T | intron_variant | Intron 7 of 90 | ENST00000389484.8 | NP_061027.2 | ||
LRP1B | XM_017004341.2 | c.624-58659G>T | intron_variant | Intron 7 of 90 | XP_016859830.1 | |||
LRP1B | XM_047444771.1 | c.1125-58659G>T | intron_variant | Intron 7 of 76 | XP_047300727.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.294 AC: 44540AN: 151696Hom.: 6774 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
44540
AN:
151696
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.294 AC: 44601AN: 151814Hom.: 6792 Cov.: 32 AF XY: 0.302 AC XY: 22365AN XY: 74174 show subpopulations
GnomAD4 genome
AF:
AC:
44601
AN:
151814
Hom.:
Cov.:
32
AF XY:
AC XY:
22365
AN XY:
74174
show subpopulations
African (AFR)
AF:
AC:
10665
AN:
41476
American (AMR)
AF:
AC:
4955
AN:
15216
Ashkenazi Jewish (ASJ)
AF:
AC:
674
AN:
3462
East Asian (EAS)
AF:
AC:
2463
AN:
5150
South Asian (SAS)
AF:
AC:
1331
AN:
4816
European-Finnish (FIN)
AF:
AC:
4252
AN:
10550
Middle Eastern (MID)
AF:
AC:
51
AN:
294
European-Non Finnish (NFE)
AF:
AC:
19421
AN:
67832
Other (OTH)
AF:
AC:
590
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1611
3223
4834
6446
8057
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
470
940
1410
1880
2350
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1242
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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