rs2302685
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_002336.3(LRP6):c.3184G>A(p.Val1062Ile) variant causes a missense change. The variant allele was found at a frequency of 0.826 in 1,612,742 control chromosomes in the GnomAD database, including 551,676 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1062T) has been classified as Uncertain significance.
Frequency
Consequence
NM_002336.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP6 | NM_002336.3 | c.3184G>A | p.Val1062Ile | missense_variant | 14/23 | ENST00000261349.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP6 | ENST00000261349.9 | c.3184G>A | p.Val1062Ile | missense_variant | 14/23 | 1 | NM_002336.3 | P1 | |
LRP6 | ENST00000543091.1 | c.3184G>A | p.Val1062Ile | missense_variant | 14/23 | 1 | |||
LRP6 | ENST00000538239.5 | c.2779G>A | p.Val927Ile | missense_variant, NMD_transcript_variant | 13/24 | 1 | |||
BCL2L14 | ENST00000298566.2 | c.*24+9985C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.843 AC: 128089AN: 151962Hom.: 54137 Cov.: 30
GnomAD3 exomes AF: 0.851 AC: 213906AN: 251378Hom.: 91377 AF XY: 0.850 AC XY: 115450AN XY: 135852
GnomAD4 exome AF: 0.825 AC: 1204333AN: 1460662Hom.: 497497 Cov.: 47 AF XY: 0.826 AC XY: 600506AN XY: 726688
GnomAD4 genome ? AF: 0.843 AC: 128190AN: 152080Hom.: 54179 Cov.: 30 AF XY: 0.846 AC XY: 62912AN XY: 74330
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at