rs3741792

Variant summary

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

The ENST00000261349.9(LRP6):​c.*4100C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,186 control chromosomes in the GnomAD database, including 251 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 0.048 ( 251 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

LRP6
ENST00000261349.9 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.378
Variant links:
Genes affected
LRP6 (HGNC:6698): (LDL receptor related protein 6) This gene encodes a member of the low density lipoprotein (LDL) receptor gene family. LDL receptors are transmembrane cell surface proteins involved in receptor-mediated endocytosis of lipoprotein and protein ligands. The protein encoded by this gene functions as a receptor or, with Frizzled, a co-receptor for Wnt and thereby transmits the canonical Wnt/beta-catenin signaling cascade. Through its interaction with the Wnt/beta-catenin signaling cascade this gene plays a role in the regulation of cell differentiation, proliferation, and migration and the development of many cancer types. This protein undergoes gamma-secretase dependent RIP- (regulated intramembrane proteolysis) processing but the precise locations of the cleavage sites have not been determined.[provided by RefSeq, Dec 2009]
BCL2L14 (HGNC:16657): (BCL2 like 14) The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. Overexpression of this gene has been shown to induce apoptosis in cells. Three alternatively spliced transcript variants encoding two distinct isoforms have been reported for this gene. [provided by RefSeq, May 2009]

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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LRP6NM_002336.3 linkuse as main transcriptc.*4100C>T 3_prime_UTR_variant 23/23 ENST00000261349.9 NP_002327.2
LRP6XM_047428844.1 linkuse as main transcriptc.*4100C>T 3_prime_UTR_variant 21/21 XP_047284800.1
LRP6NR_182264.1 linkuse as main transcriptn.7530C>T non_coding_transcript_exon_variant 25/25
LRP6XR_002957325.2 linkuse as main transcriptn.8212C>T non_coding_transcript_exon_variant 24/24

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LRP6ENST00000261349.9 linkuse as main transcriptc.*4100C>T 3_prime_UTR_variant 23/231 NM_002336.3 ENSP00000261349 P1
LRP6ENST00000538239.5 linkuse as main transcriptc.*2379C>T 3_prime_UTR_variant, NMD_transcript_variant 24/241 ENSP00000445083
BCL2L14ENST00000298566.2 linkuse as main transcriptc.711+1699G>A intron_variant, NMD_transcript_variant 2 ENSP00000298566 Q9BZR8-3

Frequencies

GnomAD3 genomes
AF:
0.0480
AC:
7306
AN:
152068
Hom.:
252
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0158
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0470
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.0186
Gnomad SAS
AF:
0.0212
Gnomad FIN
AF:
0.0777
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.0634
Gnomad OTH
AF:
0.0664
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.0480
AC:
7304
AN:
152186
Hom.:
251
Cov.:
32
AF XY:
0.0487
AC XY:
3620
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0158
Gnomad4 AMR
AF:
0.0469
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.0189
Gnomad4 SAS
AF:
0.0218
Gnomad4 FIN
AF:
0.0777
Gnomad4 NFE
AF:
0.0634
Gnomad4 OTH
AF:
0.0658
Alfa
AF:
0.0605
Hom.:
392
Bravo
AF:
0.0465
Asia WGS
AF:
0.0200
AC:
71
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.62
DANN
Benign
0.68

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: rs3741792; hg19: chr12-12269960; API