NM_000384.3(APOB):c.10740C>T (p.Asn3580=) AND not provided

Clinical significance:Benign/Likely benign (Last evaluated: Feb 1, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000589240.4

Allele description [Variation Report for NM_000384.3(APOB):c.10740C>T (p.Asn3580=)]

NM_000384.3(APOB):c.10740C>T (p.Asn3580=)

Gene:
APOB:apolipoprotein B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p24.1
Genomic location:
Preferred name:
NM_000384.3(APOB):c.10740C>T (p.Asn3580=)
HGVS:
  • NC_000002.12:g.21006128G>A
  • NG_011793.1:g.42946C>T
  • NM_000384.3:c.10740C>TMANE SELECT
  • NP_000375.3:p.Asn3580=
  • NC_000002.11:g.21229000G>A
  • NM_000384.2:c.10740C>T
Links:
dbSNP: rs150312765
NCBI 1000 Genomes Browser:
rs150312765
Molecular consequence:
  • NM_000384.3:c.10740C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000696658Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 4, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001152120CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Likely benign
(Feb 1, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696658.1

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

Description

Variant summary: The APOB c.10740C>T (p.Asn3580Asn) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 17/121204 control chromosomes at a frequency of 0.0001403, which is approximately 4 times the estimated maximal expected allele frequency of a pathogenic APOB variant (0.0000313), suggesting this variant is likely a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001152120.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 10, 2021

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