rs193920743
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_002336.3(LRP6):c.3241C>T(p.Pro1081Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000744 in 1,613,914 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1081A) has been classified as Uncertain significance.
Frequency
Consequence
NM_002336.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP6 | NM_002336.3 | c.3241C>T | p.Pro1081Ser | missense_variant | 15/23 | ENST00000261349.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP6 | ENST00000261349.9 | c.3241C>T | p.Pro1081Ser | missense_variant | 15/23 | 1 | NM_002336.3 | P1 | |
LRP6 | ENST00000543091.1 | c.3241C>T | p.Pro1081Ser | missense_variant | 15/23 | 1 | |||
LRP6 | ENST00000538239.5 | c.2836C>T | p.Pro946Ser | missense_variant, NMD_transcript_variant | 14/24 | 1 | |||
BCL2L14 | ENST00000298566.2 | c.*24+8543G>A | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251208Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135744
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727204
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74284
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at