NM_000243.3:c.333G>A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_Very_StrongBP7BS2_Supporting

The NM_000243.3(MEFV):​c.333G>A​(p.Gly111Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000593 in 1,612,880 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 3 hom., cov: 34)
Exomes 𝑓: 0.00033 ( 2 hom. )

Consequence

MEFV
NM_000243.3 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:12O:1

Conservation

PhyloP100: 0.201
Variant links:
Genes affected
MEFV (HGNC:6998): (MEFV innate immunity regulator, pyrin) This gene encodes a protein, also known as pyrin or marenostrin, that is an important modulator of innate immunity. Mutations in this gene are associated with Mediterranean fever, a hereditary periodic fever syndrome. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 16-3254735-C-T is Benign according to our data. Variant chr16-3254735-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 97517.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-3254735-C-T is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=0.201 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 SD geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MEFVNM_000243.3 linkc.333G>A p.Gly111Gly synonymous_variant Exon 2 of 10 ENST00000219596.6 NP_000234.1 O15553-2
MEFVNM_001198536.2 linkc.277+1576G>A intron_variant Intron 1 of 8 NP_001185465.2 O15553-3D2DTW2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MEFVENST00000219596.6 linkc.333G>A p.Gly111Gly synonymous_variant Exon 2 of 10 1 NM_000243.3 ENSP00000219596.1 O15553-2

Frequencies

GnomAD3 genomes
AF:
0.00316
AC:
481
AN:
152252
Hom.:
3
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0106
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00190
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.000796
AC:
197
AN:
247392
Hom.:
0
AF XY:
0.000586
AC XY:
79
AN XY:
134840
show subpopulations
Gnomad AFR exome
AF:
0.0102
Gnomad AMR exome
AF:
0.000810
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000630
Gnomad OTH exome
AF:
0.000822
GnomAD4 exome
AF:
0.000325
AC:
475
AN:
1460510
Hom.:
2
Cov.:
65
AF XY:
0.000261
AC XY:
190
AN XY:
726586
show subpopulations
Gnomad4 AFR exome
AF:
0.0108
Gnomad4 AMR exome
AF:
0.000984
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000261
Gnomad4 OTH exome
AF:
0.000646
GnomAD4 genome
AF:
0.00316
AC:
481
AN:
152370
Hom.:
3
Cov.:
34
AF XY:
0.00293
AC XY:
218
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.0105
Gnomad4 AMR
AF:
0.00190
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00156
Hom.:
0
Bravo
AF:
0.00345
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:12Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Familial Mediterranean fever Benign:3Other:1
Feb 08, 2023
Genome-Nilou Lab
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Unité médicale des maladies autoinflammatoires, CHRU Montpellier
Significance: not provided
Review Status: no classification provided
Collection Method: literature only

- -

Dec 09, 2019
Natera, Inc.
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jan 30, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:3
Jul 26, 2017
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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 -

Mar 03, 2015
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

not specified Benign:2
Jun 29, 2017
Eurofins Ntd Llc (ga)
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 10, 2020
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Acute febrile neutrophilic dermatosis Benign:1
Feb 08, 2023
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Inborn genetic diseases Benign:1
Apr 01, 2022
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Autoinflammatory syndrome Benign:1
Nov 16, 2020
Genome Diagnostics Laboratory, The Hospital for Sick Children
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Familial Mediterranean fever, autosomal dominant Benign:1
Feb 08, 2023
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
2.0
DANN
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61732425; hg19: chr16-3304735; COSMIC: COSV54822084; API