rs1003723
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000527.5(LDLR):c.1359-30C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,886 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 Uncertain significance (★).
Frequency
Consequence
NM_000527.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDLR | NM_000527.5 | c.1359-30C>A | intron_variant | Intron 9 of 17 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151886Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250150Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135338
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1460922Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 726748
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151886Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74162
ClinVar
Submissions by phenotype
Familial hypercholesterolemia Uncertain:1
This variant causes a C to A nucleotide substitution at the -30 position of intron 9 of the LDLR gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with LDLR-related disorders in the literature. This variant has been identified in 1/250150 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at