NM_000527.5:c.1359-30C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000527.5(LDLR):c.1359-30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 1,612,554 control chromosomes in the GnomAD database, including 155,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000527.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDLR | NM_000527.5 | c.1359-30C>T | intron_variant | Intron 9 of 17 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.342 AC: 51991AN: 151818Hom.: 11044 Cov.: 30
GnomAD3 exomes AF: 0.398 AC: 99474AN: 250150Hom.: 21399 AF XY: 0.405 AC XY: 54798AN XY: 135338
GnomAD4 exome AF: 0.437 AC: 638051AN: 1460618Hom.: 144400 Cov.: 37 AF XY: 0.436 AC XY: 317033AN XY: 726604
GnomAD4 genome AF: 0.342 AC: 51967AN: 151936Hom.: 11031 Cov.: 30 AF XY: 0.346 AC XY: 25688AN XY: 74250
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Benign:6
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not provided Benign:2
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not specified Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Familial hypercholesterolemia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at