ClinVar Miner

Submissions for variant NM_015627.3(LDLRAP1):c.653C>T (p.Thr218Ile)

gnomAD frequency: 0.00817  dbSNP: rs114583297
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000623146 SCV001108304 benign Hypercholesterolemia, familial, 4 2019-12-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000623146 SCV001259184 uncertain significance Hypercholesterolemia, familial, 4 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
H3Africa Consortium RCV001777171 SCV002014643 benign not specified 2020-10-28 criteria provided, single submitter research While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.08, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error.
Genetic Services Laboratory, University of Chicago RCV001777171 SCV002066177 benign not specified 2021-10-08 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000623146 SCV004564724 benign Hypercholesterolemia, familial, 4 2023-06-28 criteria provided, single submitter clinical testing
OMIM RCV000623146 SCV000740275 pathogenic Hypercholesterolemia, familial, 4 2019-06-19 no assertion criteria provided literature only
Reproductive Health Research and Development, BGI Genomics RCV000623146 SCV001142294 benign Hypercholesterolemia, familial, 4 2020-01-06 no assertion criteria provided curation NM_015627.2:c.653C>T in the LDLRAP1 gene has an allele frequency of 0.028 in African subpopulation in the gnomAD database, including 13 homozygous occurrences. It was detected in one individual with autosomal recessive hypercholesterolemia, compound heterozygous with c.863C>T (p.Ser288Leu) (PMID: 29245109). Benign computational verdict because benign predictions from DANN, DEOGEN2, EIGEN, FATHMM-MKL, MutationTaster, PrimateAI, REVEL and SIFT. Taken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BS2, BP4, PM3.
Natera, Inc. RCV001834972 SCV002085941 likely benign Familial hypercholesterolemia 2020-01-16 no assertion criteria provided clinical testing

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