NM_001136472.2(LITAF):c.27G>A (p.Ala9=) AND not provided

Clinical significance:Benign/Likely benign (Last evaluated: May 2, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_001136472.2(LITAF):c.27G>A (p.Ala9=)]

NM_001136472.2(LITAF):c.27G>A (p.Ala9=)

LITAF:lipopolysaccharide induced TNF factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001136472.2(LITAF):c.27G>A (p.Ala9=)
  • NC_000016.10:g.11556704C>T
  • NG_009008.1:g.35247G>A
  • NM_001136472.2:c.27G>AMANE SELECT
  • NM_001136473.1:c.27G>A
  • NM_004862.3:c.27G>A
  • NM_004862.4:c.27G>A
  • NP_001129944.1:p.Ala9=
  • NP_001129945.1:p.Ala9=
  • NP_004853.2:p.Ala9=
  • NP_004853.2:p.Ala9=
  • LRG_253t1:c.27G>A
  • LRG_253:g.35247G>A
  • LRG_253p1:p.Ala9=
  • NC_000016.9:g.11650560C>T
  • NR_024320.2:n.161G>A
dbSNP: rs149518815
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NR_024320.2:n.161G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001136472.2:c.27G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001136473.1:c.27G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004862.3:c.27G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004862.4:c.27G>A - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000841603Athena Diagnostics Inccriteria provided, single submitter
(May 2, 2018)
germlineclinical testing

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

SCV000984208GeneDxcriteria provided, single submitter
Likely benign
(Apr 18, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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



A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

Details of each submission

From Athena Diagnostics Inc, SCV000841603.1

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

From GeneDx, SCV000984208.1

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


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.

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

Last Updated: Oct 30, 2021

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