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NM_000527.5(LDLR):c.1887C>T (p.Phe629=) AND not specified

Germline classification:
Benign (1 submission)
Last evaluated:
Mar 4, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001192513.1

Allele description [Variation Report for NM_000527.5(LDLR):c.1887C>T (p.Phe629=)]

NM_000527.5(LDLR):c.1887C>T (p.Phe629=)

Gene:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.5(LDLR):c.1887C>T (p.Phe629=)
Other names:
NP_000518.1:p.F629F
HGVS:
  • NC_000019.10:g.11120133C>T
  • NG_009060.1:g.35753C>T
  • NM_000527.5:c.1887C>TMANE SELECT
  • NM_001195798.2:c.1887C>T
  • NM_001195799.2:c.1764C>T
  • NM_001195800.2:c.1383C>T
  • NM_001195803.2:c.1506C>T
  • NP_000518.1:p.Phe629=
  • NP_000518.1:p.Phe629=
  • NP_001182727.1:p.Phe629=
  • NP_001182728.1:p.Phe588=
  • NP_001182729.1:p.Phe461=
  • NP_001182732.1:p.Phe502=
  • LRG_274t1:c.1887C>T
  • LRG_274:g.35753C>T
  • LRG_274p1:p.Phe629=
  • NC_000019.9:g.11230809C>T
  • NM_000527.4:c.1887C>T
Links:
dbSNP: rs751234870
NCBI 1000 Genomes Browser:
rs751234870
Molecular consequence:
  • NM_000527.5:c.1887C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195798.2:c.1887C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195799.2:c.1764C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195800.2:c.1383C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195803.2:c.1506C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001360707Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Mar 4, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001360707.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The variant, LDLR c.1887C>T alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00052 in 277248 control chromosomes, predominantly at a frequency of 0.0042 within the Latino subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 3 fold of the estimated maximal expected allele frequency for a pathogenic variant in LDLR causing Familial Hypercholesterolemia phenotype (0.0013), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. To our knowledge, no occurrence of c.1887C>T in individuals affected with Familial Hypercholesterolemia and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024