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NM_153240.5(NPHP3):c.65C>T (p.Ala22Val) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jul 27, 2023
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:
RCV000596794.6

Allele description [Variation Report for NM_153240.5(NPHP3):c.65C>T (p.Ala22Val)]

NM_153240.5(NPHP3):c.65C>T (p.Ala22Val)

Genes:
LOC129937586:ATAC-STARR-seq lymphoblastoid silent region 14743 [Gene]
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.65C>T (p.Ala22Val)
HGVS:
  • NC_000003.12:g.132722291G>A
  • NG_008130.2:g.5142C>T
  • NM_153240.5:c.65C>TMANE SELECT
  • NP_694972.3:p.Ala22Val
  • NC_000003.11:g.132441135G>A
  • NG_008130.1:g.5142C>T
  • NM_153240.4:c.65C>T
  • NR_002811.2:n.542G>A
  • NR_037804.1:n.169C>T
  • NR_152743.1:n.542G>A
Protein change:
A22V
Links:
dbSNP: rs369447363
NCBI 1000 Genomes Browser:
rs369447363
Molecular consequence:
  • NM_153240.5:c.65C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_002811.2:n.542G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_037804.1:n.169C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_152743.1:n.542G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000707043Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Uncertain significance
(Dec 5, 2017) 		germlineclinical testing

Citation Link,

SCV005078506GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(Jul 27, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown2not providednot providednot providednot providedclinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000707043.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV005078506.1

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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

Last Updated: Oct 13, 2024