2-169242963-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004525.3(LRP2):c.3660A>T(p.Ala1220=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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. Synonymous variant affecting the same amino acid position (i.e. A1220A) has been classified as Benign.
Frequency
Consequence
NM_004525.3 synonymous
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 |
---|---|---|---|---|---|---|---|
LRP2 | NM_004525.3 | c.3660A>T | p.Ala1220= | synonymous_variant | 24/79 | ENST00000649046.1 | |
LRP2 | XM_011511183.4 | c.3660A>T | p.Ala1220= | synonymous_variant | 24/78 | ||
LRP2 | XM_047444340.1 | c.2736A>T | p.Ala912= | synonymous_variant | 24/79 | ||
LRP2 | XM_011511184.3 | c.1371A>T | p.Ala457= | synonymous_variant | 9/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP2 | ENST00000649046.1 | c.3660A>T | p.Ala1220= | synonymous_variant | 24/79 | NM_004525.3 | P1 | ||
LRP2 | ENST00000443831.1 | c.3249A>T | p.Ala1083= | synonymous_variant | 22/23 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at