NM_000243.3(MEFV):c.-15C>G AND not specified

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Oct 4, 2022
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:: RCV000438166.15

Allele description [Variation Report for NM_000243.3(MEFV):c.-15C>G]

NM_000243.3(MEFV):c.-15C>G

Gene:

MEFV:MEFV innate immunity regulator, pyrin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000243.3(MEFV):c.-15C>G

HGVS:

NC_000016.10:g.3256602G>C
NG_007871.1:g.5026C>G
NM_000243.3:c.-15C>GMANE SELECT
NM_001198536.2:c.-15C>G
LRG_190t1:c.-15C>G
LRG_190:g.5026C>G
NC_000016.9:g.3306602G>C
NM_000243.2:c.-15C>G

Links:

dbSNP: rs11466015

NCBI 1000 Genomes Browser:

rs11466015

Molecular consequence:

NM_000243.3:c.-15C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001198536.2:c.-15C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Lactase-phlorizin hydrolase [Cricetulus griseus]
Lactase-phlorizin hydrolase [Cricetulus griseus]
gi|344244844|gb|EGW00948.1||gnl|WGS |I79_003354

Protein
lactase [Rattus norvegicus]
lactase [Rattus norvegicus]
gi|149058719|gb|EDM09876.1||gnl|WGS |rCP33899

Protein
1DWA (3)
Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001159771	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Apr 23, 2019)	germline	clinical testing	Citation Link,
SCV001482170	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Oct 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001159771

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely benign
(Apr 23, 2019)

germline

clinical testing

Citation Link,

SCV001482170

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Oct 4, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001159771.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001482170.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: MEFV c.-15C>G is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.0035 in 150986 control chromosomes, predominantly at a frequency of 0.012 within the African or African-American subpopulation, including 3 homozygotes (gnomAD v3.1, genomes dataset). This frequency is somewhat lower than the estimated maximum expected for a pathogenic variant in MEFV causing Familial Mediterranean Fever (0.022), allowing no clear conclusion about variant significance. To our knowledge, no occurrence of c.-15C>G in individuals affected with Familial Mediterranean Fever and no experimental evidence demonstrating its impact on protein function have been reported. Four other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as VUS (n=2) or likely benign (n=2). Based on the evidence outlined above, the variant was classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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