rs869320644
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_002336.3(LRP6):āc.2995G>Cā(p.Gly999Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002336.3 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRP6 | NM_002336.3 | c.2995G>C | p.Gly999Arg | missense_variant, splice_region_variant | 14/23 | ENST00000261349.9 | NP_002327.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP6 | ENST00000261349.9 | c.2995G>C | p.Gly999Arg | missense_variant, splice_region_variant | 14/23 | 1 | NM_002336.3 | ENSP00000261349 | P1 | |
LRP6 | ENST00000543091.1 | c.2995G>C | p.Gly999Arg | missense_variant, splice_region_variant | 14/23 | 1 | ENSP00000442472 | |||
LRP6 | ENST00000538239.5 | c.2590G>C | p.Gly864Arg | missense_variant, splice_region_variant, NMD_transcript_variant | 13/24 | 1 | ENSP00000445083 | |||
BCL2L14 | ENST00000298566.2 | c.*24+10174C>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000298566 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461114Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 726912
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Orofacial cleft Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | Mar 10, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at