12-12121146-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_002336.3(LRP6):c.4822C>T(p.Pro1608Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,574 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1608L) has been classified as Uncertain significance.
Frequency
Consequence
NM_002336.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP6 | NM_002336.3 | c.4822C>T | p.Pro1608Ser | missense_variant | 23/23 | ENST00000261349.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP6 | ENST00000261349.9 | c.4822C>T | p.Pro1608Ser | missense_variant | 23/23 | 1 | NM_002336.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460574Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726540
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Keratoconus Uncertain:1
Uncertain significance, no assertion criteria provided | research | Institute of Human Genetics, Polish Academy of Sciences | Feb 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at