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NM_001065.4(TNFRSF1A):c.36A>G (p.Pro12=) AND not specified

Germline classification:
Benign (5 submissions)
Last evaluated:
Nov 12, 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:
RCV000252192.24

Allele description [Variation Report for NM_001065.4(TNFRSF1A):c.36A>G (p.Pro12=)]

NM_001065.4(TNFRSF1A):c.36A>G (p.Pro12=)

Gene:
TNFRSF1A:TNF receptor superfamily member 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p13.31
Genomic location:
Preferred name:
NM_001065.4(TNFRSF1A):c.36A>G (p.Pro12=)
HGVS:
  • NC_000012.12:g.6341779T>C
  • NG_007506.1:g.5317A>G
  • NM_001065.4:c.36A>GMANE SELECT
  • NM_001346091.2:c.-135A>G
  • NM_001346092.2:c.-542A>G
  • NP_001056.1:p.Pro12=
  • NP_001056.1:p.Pro12=
  • LRG_193t1:c.36A>G
  • LRG_193:g.5317A>G
  • LRG_193p1:p.Pro12=
  • NC_000012.11:g.6450945T>C
  • NM_001065.3:c.36A>G
  • NR_144351.2:n.298A>G
  • p.Pro12Pro
Links:
dbSNP: rs767455
NCBI 1000 Genomes Browser:
rs767455
Molecular consequence:
  • NM_001346091.2:c.-135A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001346092.2:c.-542A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_144351.2:n.298A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001065.4:c.36A>G - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
57

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
SCV000306334PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benigngermlineclinical testing

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

SCV000540560Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Benign
(Mar 28, 2016)
germlineclinical testing

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

SCV001744757Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Benigngermlineclinical testing

SCV001929573Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV004102023Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Nov 12, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineno57not providednot providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

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 PreventionGenetics, part of Exact Sciences, SCV000306334.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000540560.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency

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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001744757.3

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001929573.1

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

From Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan, SCV004102023.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided57not providednot providedclinical testing PubMed (1)

Description

This variant is classified as Benign based on local population frequency. This variant was detected in 59% of patients studied by a panel of primary immunodeficiencies. Number of patients: 57. Only high quality variants are reported.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot provided57not providednot providednot provided

Last Updated: Jul 15, 2024