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NM_153240.5(NPHP3):c.393+18C>T AND not specified

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Dec 1, 2016
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:
RCV000421605.3

Allele description [Variation Report for NM_153240.5(NPHP3):c.393+18C>T]

NM_153240.5(NPHP3):c.393+18C>T

Genes:
NPHP3-AS1:NPHP3 antisense RNA 1 [Gene - HGNC]
NPHP3-ACAD11:NPHP3-ACAD11 readthrough (NMD candidate) [Gene - HGNC]
NPHP3:nephrocystin 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q22.1
Genomic location:
Preferred name:
NM_153240.5(NPHP3):c.393+18C>T
HGVS:
  • NC_000003.12:g.132721945G>A
  • NG_008130.2:g.5488C>T
  • NM_153240.5:c.393+18C>TMANE SELECT
  • NC_000003.11:g.132440789G>A
  • NG_008130.1:g.5488C>T
  • NM_153240.4:c.393+18C>T
  • NR_002811.2:n.196G>A
  • NR_152743.1:n.196G>A
Links:
dbSNP: rs367765709
NCBI 1000 Genomes Browser:
rs367765709
Molecular consequence:
  • NM_153240.5:c.393+18C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_002811.2:n.196G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_152743.1:n.196G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000533873GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Likely benign
(Dec 1, 2016)
germlineclinical testing

Citation Link,

SCV001978814Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000533873.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001978814.1

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

Last Updated: Feb 28, 2024