rs3741792
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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
ENST00000261349.9 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.378
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]
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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 |
---|---|---|---|---|---|---|---|---|
LRP6 | NM_002336.3 | c.*4100C>T | 3_prime_UTR_variant | 23/23 | ENST00000261349.9 | NP_002327.2 | ||
LRP6 | XM_047428844.1 | c.*4100C>T | 3_prime_UTR_variant | 21/21 | XP_047284800.1 | |||
LRP6 | NR_182264.1 | n.7530C>T | non_coding_transcript_exon_variant | 25/25 | ||||
LRP6 | XR_002957325.2 | n.8212C>T | non_coding_transcript_exon_variant | 24/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP6 | ENST00000261349.9 | c.*4100C>T | 3_prime_UTR_variant | 23/23 | 1 | NM_002336.3 | ENSP00000261349 | P1 | ||
LRP6 | ENST00000538239.5 | c.*2379C>T | 3_prime_UTR_variant, NMD_transcript_variant | 24/24 | 1 | ENSP00000445083 | ||||
BCL2L14 | ENST00000298566.2 | c.711+1699G>A | intron_variant, NMD_transcript_variant | 2 | ENSP00000298566 |
Frequencies
GnomAD3 genomes AF: 0.0480 AC: 7306AN: 152068Hom.: 252 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome AF: 0.0480 AC: 7304AN: 152186Hom.: 251 Cov.: 32 AF XY: 0.0487 AC XY: 3620AN XY: 74390
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at