VCV000097517.34 - ClinVar

NM_000243.3(MEFV):c.333G>A (p.Gly111=)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(13)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000243.3(MEFV):c.333G>A (p.Gly111=)

Variation ID: 97517 Accession: VCV000097517.34

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 16p13.3 16: 3254735 (GRCh38) [ NCBI UCSC ] 16: 3304735 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 20, 2014	Sep 29, 2024	Jan 30, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000243.3:c.333G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000234.1:p.Gly111=	synonymous
NM_001198536.2:c.277+1576G>A		intron variant
NC_000016.10:g.3254735C>T
NC_000016.9:g.3304735C>T
NG_007871.1:g.6893G>A
LRG_190:g.6893G>A
LRG_190t1:c.333G>A	LRG_190p1:p.Gly111=

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000016.10:3254734:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00459 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD), exomes 0.00080

The Genome Aggregation Database (gnomAD) 0.00339

Trans-Omics for Precision Medicine (TOPMed) 0.00345

1000 Genomes Project 0.00459

Exome Aggregation Consortium (ExAC) 0.00081

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00249

1000 Genomes Project 30x 0.00484

Links

ClinGen: CA280588 dbSNP: rs61732425 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
MEFV		No evidence available	No evidence available	GRCh38 GRCh37	961	1262

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Familial Mediterranean fever	Benign/Likely benign (4)	criteria provided, multiple submitters, no conflicts	Jan 30, 2024	RCV000083769.17
not specified	Benign/Likely benign (2)	criteria provided, multiple submitters, no conflicts	Jul 10, 2020	RCV000593418.5
not provided	Benign/Likely benign (3)	criteria provided, multiple submitters, no conflicts	Jul 26, 2017	RCV000756331.13
Autoinflammatory syndrome	Likely benign (1)	criteria provided, single submitter	Nov 16, 2020	RCV002262645.3
Inborn genetic diseases	Likely benign (1)	criteria provided, single submitter	Apr 1, 2022	RCV002321582.2
Acute febrile neutrophilic dermatosis	Benign (1)	criteria provided, single submitter	Feb 8, 2023	RCV003126474.1
Familial Mediterranean fever, autosomal dominant	Benign (1)	criteria provided, single submitter	Feb 8, 2023	RCV003126473.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (Jun 29, 2017)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000709301.2 First in ClinVar: Apr 02, 2018 Last updated: Apr 02, 2018	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MEFV Number of individuals with the variant: 1 Zygosity: Single Heterozygote Sex: mixed
Likely benign (Nov 16, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Autoinflammatory syndrome Affected status: yes Allele origin: germline	Genome Diagnostics Laboratory, The Hospital for Sick Children Accession: SCV002543755.1 First in ClinVar: Jul 09, 2022 Last updated: Jul 09, 2022
Likely benign (Jul 26, 2017)	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process) Method: clinical testing	Not Provided Affected status: unknown Allele origin: germline	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories Accession: SCV000884108.1 First in ClinVar: Feb 18, 2019 Last updated: Feb 18, 2019	Comment: The MEFV c.333G>A;p.Gly111Gly variant has not been described in the medical literature, but is listed in a gene-specific database in a symptomatic individual (see link). … (more) The MEFV c.333G>A;p.Gly111Gly variant has not been described in the medical literature, but is listed in a gene-specific database in a symptomatic individual (see link). The variant is listed in the ClinVar database (Variation ID: 97517) and the dbSNP variant database (rs61732425) with an allele frequency of up to 0.7373 percent (32/4308 alleles) in the African American population in the Exome Variant Server and up to 1.081 percent in the African population in the Genome Aggregation Consortium (251/23226 alleles, 2 homozygotes). The nucleotide at this position is weakly conserved and computational algorithms (SpliceSiteFinder-like, MaxEntScan, NNSplice, GeneSplicer, Human Splicing Finder) predict this variant does not significantly alter splicing. Considering available information, this variant is classified as likely benign. References: Link to Infevers database: http://fmf.igh.cnrs.fr/ISSAID/infevers/search.php?n=1 (less)
Likely benign (Jul 10, 2020)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV001426904.1 First in ClinVar: Aug 09, 2020 Last updated: Aug 09, 2020	Publications: PubMed (1) PubMed: 19790133
Benign (Mar 03, 2015)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001891062.1 First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021
Benign (Feb 08, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Familial Mediterranean fever, autosomal dominant Affected status: unknown Allele origin: germline	Genome-Nilou Lab Accession: SCV003802414.1 First in ClinVar: Feb 18, 2023 Last updated: Feb 18, 2023
Benign (Feb 08, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Acute febrile neutrophilic dermatosis Affected status: unknown Allele origin: germline	Genome-Nilou Lab Accession: SCV003802415.1 First in ClinVar: Feb 18, 2023 Last updated: Feb 18, 2023
Likely benign (Feb 08, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Familial Mediterranean fever Affected status: unknown Allele origin: germline	Genome-Nilou Lab Accession: SCV003802413.1 First in ClinVar: Feb 18, 2023 Last updated: Feb 18, 2023
Benign (Jan 30, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Familial Mediterranean fever Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000629044.9 First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024
Likely benign (Apr 01, 2022)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV002605620.2 First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024	Comment: This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more) This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
Likely benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005215127.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Likely benign (Dec 09, 2019)	no assertion criteria provided Method: clinical testing	Familial Mediterranean fever Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV002087469.1 First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022
not provided (-)	no classification provided Method: not provided	Familial Mediterranean fever Affected status: not provided Allele origin: unknown	Unité médicale des maladies autoinflammatoires, CHRU Montpellier Accession: SCV000115865.1 First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014
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Comment:

The MEFV c.333G>A;p.Gly111Gly variant has not been described in the medical literature, but is listed in a gene-specific database in a symptomatic individual (see link). The variant is listed in the ClinVar database (Variation ID: 97517) and the dbSNP variant database (rs61732425) with an allele frequency of up to 0.7373 percent (32/4308 alleles) in the African American population in the Exome Variant Server and up to 1.081 percent in the African population in the Genome Aggregation Consortium (251/23226 alleles, 2 homozygotes). The nucleotide at this position is weakly conserved and computational algorithms (SpliceSiteFinder-like, MaxEntScan, NNSplice, GeneSplicer, Human Splicing Finder) predict this variant does not significantly alter splicing. Considering available information, this variant is classified as likely benign. References: Link to Infevers database: http://fmf.igh.cnrs.fr/ISSAID/infevers/search.php?n=1

Comment:

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Familial mediterranean Fever in the world.	Ben-Chetrit E	Arthritis and rheumatism	2009	PMID: 19790133
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MEFV	-	-	-	-

Text-mined citations for rs61732425 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_000243.3(MEFV):c.333G>A (p.Gly111=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs61732425 ...