NC_000019.10:g.11089396C>T AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 17, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001508836.18

Allele description [Variation Report for NC_000019.10:g.11089396C>T]

NC_000019.10:g.11089396C>T

Genes:

LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
LDLR-AS1:LDLR antisense RNA 1 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NC_000019.10:g.11089396C>T

HGVS:

NC_000019.10:g.11089396C>T
NG_009060.1:g.5016C>T
NM_000527.4:c.-153C>T
NM_001195798.1:c.-153C>T
NM_001195799.1:c.-153C>T
NM_001195800.1:c.-153C>T
NM_001195803.1:c.-153C>T
LRG_274t1:c.-153C>T
LRG_274:g.5016C>T
NC_000019.9:g.11200072C>T
NR_163945.1:n.264G>A
c.-153C>T

Links:

LDLR-LOVD, British Heart Foundation: LDLR_001116; dbSNP: rs879254366

NCBI 1000 Genomes Browser:

rs879254366

Molecular consequence:

NR_163945.1:n.264G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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RecName: Full=Calsyntenin-1; AltName: Full=Alcadein-alpha; Short=Alc-alpha; Cont...
RecName: Full=Calsyntenin-1; AltName: Full=Alcadein-alpha; Short=Alc-alpha; Contains: RecName: Full=Soluble Alc-alpha; Short=SAlc-alpha; Contains: RecName: Full=CTF1-alpha; AltName: Full=C-terminal fragment 1-alpha; Flags: Precursor
gi|23396509|sp|Q9EPL2.1|CSTN1_MOUSE

Protein
EVC [Pseudorca crassidens]
EVC [Pseudorca crassidens]
Gene ID:137223540

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001715231	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 3, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001871090	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jul 17, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001715231

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 3, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001871090

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jul 17, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV001715231.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV001871090.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Published functional studies suggest a damaging effect through impaired promoter activity (PMID: 31395865); Reliable data are not available in large population cohorts to assess the frequency of this variant in publicly available databases; however, this variant has not been detected at significant frequency in presumably healthy individuals tested at GeneDx.; Also known as c.-60C>T; This variant is associated with the following publications: (PMID: 17625505, 23315997, 15303010, 21310417, 22698793, 35052492, 38955586, 31395865)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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