rs3923350

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018557.3(LRP1B):​c.9425+3314C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,968 control chromosomes in the GnomAD database, including 4,996 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 0.25 ( 4996 hom., cov: 31)

Consequence

LRP1B
NM_018557.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.692
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRP1BNM_018557.3 linkuse as main transcriptc.9425+3314C>A intron_variant ENST00000389484.8
LRP1BXM_017004341.2 linkuse as main transcriptc.9035+3314C>A intron_variant
LRP1BXM_017004342.1 linkuse as main transcriptc.4277+3314C>A intron_variant
LRP1BXM_047444771.1 linkuse as main transcriptc.9536+3314C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LRP1BENST00000389484.8 linkuse as main transcriptc.9425+3314C>A intron_variant 1 NM_018557.3 P1

Frequencies

GnomAD3 genomes
AF:
0.248
AC:
37650
AN:
151850
Hom.:
4997
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.198
Gnomad AMI
AF:
0.277
Gnomad AMR
AF:
0.378
Gnomad ASJ
AF:
0.348
Gnomad EAS
AF:
0.242
Gnomad SAS
AF:
0.171
Gnomad FIN
AF:
0.214
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.253
Gnomad OTH
AF:
0.289
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.248
AC:
37669
AN:
151968
Hom.:
4996
Cov.:
31
AF XY:
0.246
AC XY:
18302
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.198
Gnomad4 AMR
AF:
0.378
Gnomad4 ASJ
AF:
0.348
Gnomad4 EAS
AF:
0.241
Gnomad4 SAS
AF:
0.171
Gnomad4 FIN
AF:
0.214
Gnomad4 NFE
AF:
0.253
Gnomad4 OTH
AF:
0.295
Alfa
AF:
0.262
Hom.:
7343
Bravo
AF:
0.264
Asia WGS
AF:
0.221
AC:
767
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.41
DANN
Benign
0.33

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3923350; hg19: chr2-141239598; API