2-169212054-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004525.3(LRP2):āc.6194T>Gā(p.Ile2065Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 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. I2065T) has been classified as Benign.
Frequency
Consequence
NM_004525.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRP2 | NM_004525.3 | c.6194T>G | p.Ile2065Ser | missense_variant | 37/79 | ENST00000649046.1 | NP_004516.2 | |
LRP2 | XM_011511183.4 | c.6194T>G | p.Ile2065Ser | missense_variant | 37/78 | XP_011509485.1 | ||
LRP2 | XM_047444340.1 | c.5270T>G | p.Ile1757Ser | missense_variant | 37/79 | XP_047300296.1 | ||
LRP2 | XM_011511184.3 | c.3905T>G | p.Ile1302Ser | missense_variant | 22/64 | XP_011509486.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251076Hom.: 1 AF XY: 0.0000147 AC XY: 2AN XY: 135680
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000137 AC: 2AN: 1461766Hom.: 1 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727202
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at