rs753151497
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The ENST00000374338.5(LDLRAP1):c.863C>T(p.Ser288Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,452 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. S288S) has been classified as Likely benign.
Frequency
Consequence
ENST00000374338.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDLRAP1 | NM_015627.3 | c.863C>T | p.Ser288Leu | missense_variant | 9/9 | ENST00000374338.5 | NP_056442.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LDLRAP1 | ENST00000374338.5 | c.863C>T | p.Ser288Leu | missense_variant | 9/9 | 1 | NM_015627.3 | ENSP00000363458 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249856Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135430
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461262Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726956
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74350
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 19, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at