rs75977701

chr16-3254158-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3 BP6 BS1 BS2

The NM_000243.3(MEFV):c.910G>A(p.Gly304Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,613,990 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/24 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0034 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0021 (32 hom.)
• Consequence: MEFV NM_000243.3 missense, splice_region
• Scores: Splicing: ADA: 0.9978
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:7 B:6 O:1
• Conservation: PhyloP100: 0.0780

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• BP6: Variant 16-3254158-C-T is Benign according to our data. Variant chr16-3254158-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 36513.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Benign=2, not_provided=1, Uncertain_significance=6}. Variant chr16-3254158-C-T is described in Lovd as [Likely_benign]. Variant chr16-3254158-C-T is described in Lovd as [Benign].
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0034 (518/152332) while in subpopulation EAS AF= 0.0224 (116/5180). AF 95% confidence interval is 0.0191. There are 3 homozygotes in gnomad4. There are 338 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 3 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEFV	NM_000243.3	c.910G>A	p.Gly304Arg	missense_variant, splice_region_variant	2/10	ENST00000219596.6
MEFV	NM_001198536.2	c.277+2153G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEFV	ENST00000219596.6	c.910G>A	p.Gly304Arg	missense_variant, splice_region_variant	2/10	1	NM_000243.3	P3

Frequencies

GnomAD3 genomes AF: 0.00340 AC: 518 AN: 152214 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.000868

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000500

Gnomad OTH AF: 0.00334

GnomAD3 exomes AF: 0.00458 AC: 1144 AN: 249962 Hom.: 12 AF XY: 0.00430 AC XY: 582 AN XY: 135264

Gnomad AFR exome AF: 0.000741

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00427

Gnomad EAS exome AF: 0.0180

Gnomad SAS exome AF: 0.00108

Gnomad FIN exome AF: 0.0272

Gnomad NFE exome AF: 0.000934

Gnomad OTH exome AF: 0.00556

GnomAD4 exome AF: 0.00209 AC: 3058 AN: 1461658 Hom.: 32 Cov.: 31 AF XY: 0.00211 AC XY: 1534 AN XY: 727136

Gnomad4 AFR exome AF: 0.000388

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00429

Gnomad4 EAS exome AF: 0.0222

Gnomad4 SAS exome AF: 0.00136

Gnomad4 FIN exome AF: 0.0263

Gnomad4 NFE exome AF: 0.000289

Gnomad4 OTH exome AF: 0.00340

GnomAD4 genome AF: 0.00340 AC: 518 AN: 152332 Hom.: 3 Cov.: 32 AF XY: 0.00454 AC XY: 338 AN XY: 74498

Gnomad4 AFR AF: 0.000914

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.000500

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00149 Hom.: 2

Bravo AF: 0.00138

ESP6500AA AF: 0.000228 AC: 1

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.00429 AC: 521

Asia WGS AF: 0.0200 AC: 69 AN: 3478

EpiCase AF: 0.000164

EpiControl AF: 0.000119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:7 Benign:6 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:4 Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	MEFV: PP3, BS1, BS2 -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Apr 26, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 20, 2023	The MEFV c.910G>A; p.Gly304Arg variant (rs75977701) is reported in the literature in individuals affected with atypical familial Mediterranean fever (Arasawa 2012, Gunesacar 2014, Kishida 2014, Migita 2014), but also in healthy controls (Migita 2012, Nonaka 2015, Oshima 2010, Taniuchi 2013). This variant is reported with conflicting interpretations of pathogenicity in ClinVar (Variation ID: 36513), and is found in the general population with an overall allele frequency of 0.47% (1318/281346 alleles, including 12 homozygotes), with an increased frequency in the Finnish European population of 2.7% (686/25046 alleles) in the Genome Aggregation Database. Computational analyses predict that this variant is neutral (REVEL: 0.055). However, this variant resides in the last nucleotide of exon 2, and is predicted to disrupt the canonical splice donor site (Alamut v.2.11), with functional studies supporting a negative impact on gene function (Tone 2012). Due to conflicting information, the clinical significance of the p.Gly304Arg variant is uncertain at this time. References: Arasawa S et al. Mediterranean mimicker. Lancet. 2012 380(9858):2052. PMID: 23217869. Gunesacar R et al. Frequency of MEFV gene mutations in Hatay province, Mediterranean region of Turkey and report of a novel missense mutation (I247V). Gene. 2014 546(2):195-9. PMID: 24929125. Kishida D et al. Genotype-phenotype correlation in Japanese patients with familial Mediterranean fever: differences in genotype and clinical features between Japanese and Mediterranean populations. Arthritis Res Ther. 2014 16(5):439. PMID: 25261100. Migita K et al. Clinical relevance of MEFV gene mutations in Japanese patients with unexplained fever. J Rheumatol. 2012 Apr;39(4):875-7. PMID: 22467954. Migita K et al. Coexistence of familial Mediterranean fever and rheumatoid arthritis. Mod Rheumatol. 2014 24(1): 212-6. PMID: 24261781. Nonaka F et al. Increased prevalence of MEFV exon 10 variants in Japanese patients with adult-onset Still's disease. Clin Exp Immunol. 2015 Mar;179(3):392-7. PMID: 25286988. Oshima K et al. A case of familial Mediterranean fever associated with compound heterozygosity for the pyrin variant L110P-E148Q/M680I in Japan. Mod Rheumatol. 2010 Apr;20(2):193-5. PMID: 19967574. Taniuchi S et al. MEFV Variants in Patients with PFAPA Syndrome in Japan. Open Rheumatol J. 2013 7:22-5. PMID: 23847694. Tone Y et al. Enhanced exon 2 skipping caused by c.910G>A variant and alternative splicing of MEFV genes in two independent cases of familial Mediterranean fever. Mod Rheumatol. 2012 22(1):45-51. PMID: 21562927. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Dec 12, 2022	Reported in the presence of other MEFV variants in individuals with familial Mediterranean fever or unexplained fevers in published literature; however, many of these variants are of uncertain clinical significance (Migita et al., 2012; Kishida et al., 2014); Published functional studies suggest that variant alters gene splicing with skipping of exon 2, while the functional consequences of the resulting truncated protein product remain unknown and loss-of-function is not an established mechanism of disease (Tone et al., 2012); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in cis with a pathogenic MEFV variant in at least one family referred for genetic testing at GeneDx; This variant is associated with the following publications: (PMID: 28943464, 28863210, 32398039, 31401792, 23847694, 26933204, 23437051, 24965843, 24261781, 25525159, 21562927, 25671271, 24929125, 19967574, 23588594, 25261100, 23217869, 25286988, 25088882, 22467954, 25703702, 23137073, 30235678, 31155445, 31494649, 31682063, 32082075, 29178647, 31998953, 31989427, 31803701, 32824452, 31342094, 32115236, 33974187, Sargin[case report], 34177904, Tomokawa[other], 33733382, 34904166) -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The MEFV p.Gly304Arg variant has been reported many times in the literature in relation multiple phenotypes, mainly familial Mediterranean fever (FMF) or phenotypes involving reoccuring fevers, as well as rheumatic disease and other autoimmune phenotypes, however the variant has also been reported to a large extent in healthy control populations (Ebrahimi-Fakhari_2012_PMID: 23137073; Arasawa_2012_PMID: 23217869; Migita_2013_PMID: 23437051; Gunesacar_2014_PMID: 24929125; Yoshioka_2014_PMID: 25088882; Migita_2014_PMID: 24261781; Comak_2014_PMID: 23588594; Fujikawa_2014_PMID: 24965843; Jo_2015_PMID: 25671271; Moritake_2016_ PMID: 26933204; Nonaka_2015_PMID: 25286988; Taniuchi_2013_PMID: 23847694). The variant was identified in 11/384 alleles (freq=0.029) from patients with sure or probable FMF, 19/818 alleles (freq=0.023) from patients with unexplained fever but with an unlikely diagnosis of FMF and in 6/210 alleles (freq=0.029) from healthy controls (Migita_2016_PMID: 27473114). Another study identified the G304R variant in 2/116 patients with FMF as a complex compound heterozygous allele as these patients each carried two other MEFV variants (Kishida_2014_ PMID: 25261100). A study that performed mutational analysis of the MEFV gene on a patient with periodic fever and chest pain who was suspected to have FMF identified the G304R variant only in the patient's healthy mother and sister but not in the affected patient (Oshima_2009_19967574). However, a functional study identified two cases of FMF that were homozygous for the G304R variant and found that the variant caused excessive exon 2 skipping due to alternative splicing in these patients, suggesting that this abberant splicing was causal of thier phenotype. Transfection of wild-type and  G304R variant MEFV constructs into HEK293T cells resulted in aberrant splicing of the mutant construct leading to abnormal protein size, presumably causing loss of pyrin function (Tone_2012_ PMID: 21562927). This p.G304R was also identified in dbSNP (ID: rs75977701), ClinVar (classified as benign by Invitae, likely benign by Counsyl, likely pathogenic by GeneDx and as a VUS by ARUP Laboratories and Integrated Genetics), Cosmic (FATHMM prediction of neutral; score=0.00) and LOVD 3.0. The variant was identified in control databases in 1318 of 281346 chromosomes (12 homozygous) at a frequency of 0.004685 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (Finnish) in 686 of 25046 chromosomes (freq: 0.02739), East Asian in 360 of 19930 chromosomes (freq: 0.01806), Other in 46 of 7206 chromosomes (freq: 0.006384), Ashkenazi Jewish in 43 of 10360 chromosomes (freq: 0.004151), South Asian in 33 of 30606 chromosomes (freq: 0.001078), European (non-Finnish) in 130 of 127858 chromosomes (freq: 0.001017) and African in 20 of 24910 chromosomes (freq: 0.000803); it was not observed in the Latino population. The p.Gly304Arg variant occurs in the last base of the exon; this position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. Further,  4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict the loss of the 5' splice site. The functional study by Tone et al. described above also confirmed this abberant splicing prediction (Tone_2012_ PMID: 21562927). However, the p.Gly304 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain signi -

Familial Mediterranean fever Uncertain:1 Benign:2 Other:1

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 26, 2024	- -
not provided, no classification provided	literature only	Unité médicale des maladies autoinflammatoires, CHRU Montpellier	-	- -
Likely benign, criteria provided, single submitter	literature only	Counsyl	Dec 11, 2014	- -

not specified Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 16, 2023	Variant summary: MEFV c.910G>A (p.Gly304Arg) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant also alters a non-conserved nucleotide, positioned as the last nucleotide of exon 2 adjacent to the canonical splice donor site of intron 2. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes the canonical 5' splicing donor site. Two predict the variant weakens the canonical 5' splicing donor site. These predictions are supported by at least one publication which demonstrated that the variant increases the in-frame skipping of exon 2 in patients PBMCs, due to enhanced alternative splicing (Tone_2012). Authors transfected the normal and variant MEFV genes into HEK293T (embryonic kidney origin) cells, however the transfectants (i.e. both the full-length mutant containing the G304R missense change, and the exon 2 deleted short isoform) failed to show altered intracellular pyrin distribution in this cell type. As the cell system used by the authors may not represent a physiological cell type, the functional significance of this variant remains unclear at the cellular and/or organismal level. The variant allele was found at a frequency of 0.0046 in 250756 control chromosomes, predominantly at a frequency of 0.018 within the East Asian subpopulation in the gnomAD database, including 12 homozygotes. Additionally, the variant was reported with even higher frequencies in the 1000 Genomes Project within some East Asian subpopulations (e.g. in Chinese Dai in Xishuangbanna (CDX) 5.4%, Han Chinese in Beijing (CHB) 2.4%, Japanese in Tokyo (JPT) 2.9%, Kinh in Ho Chi Minh City in Vietnam (KHV) 2.5%), suggesting this variant is likely a benign polymorphism (Moradian_2017). Though the variant, c.910G>A, has been reported in the literature in individuals affected with Familial Mediterranean Fever (FMF) (example, Arasawa_2012, Comak_2013, Coskun_2015, Ebrahmi-Fakhari_2012, Fujikawa_2014, Gunesacar_2014, Jo_2015, Kishida_2014, Migita_2012, Migita_2014, Migita_2013, Oshima_2010, Tone_2012, Yoshioka_2014, Migita_2016, Moritake_2016, Erdem_2017, Ebadi_2017, Hara_2018, Dundar_2022), a recent study evaluating the prevalence of the disease in the Japanese population (Migita_2016) found similar allele frequencies among FMF patients (2.9%; 11/384 alleles) and healthy subjects (2.9%; 6/210 alleles). This frequency among healthy Japanese controls is comparable to that reported in large Japanese control population databases (i.e. 2.6% in jMorp, and 2% in HGVD). A functional study analyzed the effects of certain MEFV variants on cell death with or without stimulation with Clostridium difficile toxin A (TcdA) or UCN-01A and concluded that p.Gly304Arg conferred no substantial increase in cell death (Honda_2021). Additionally, in 2018 the experts international study group for systemic autoinflammatory diseases (INSAID) reported a validated classification of likely benign for the variant (Van Gijn_2018). One ClinVar submitter (evaluation after 2014) cites the variant as benign and three ClinVar submitters (evaluation after 2014) cite it as uncertain significance. At-least one submitter has re-classified this variant from a likely pathogenic to a VUS outcome since its previous evaluation. Based on the evidence outlined above, the variant was classified as likely benign. -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Autoinflammatory syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Apr 01, 2020

- -

MEFV-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 11, 2023

The MEFV c.910G>A variant is predicted to result in the amino acid substitution p.Gly304Arg. This variant has been reported in patients with familial mediterranean fever (Tone et al. 2012. PubMed ID: 21562927; Ebadi et al. 2017. PubMed ID: 28943464) and in a patient with Sweets syndrome, myelodyplastic syndrome, high fever and leukocytosis (Jo et al. 2015. PubMed ID: 25671271). The c.910G>A substitution resides near the consensus intron 2 splice donor site and is predicted to abolish this splice donor site (Alamut v.2.11). Biochemical analysis in one report indicates that the c.910G>A substitution causes aberrant exon splicing and results in a truncated MEFV protein (Tone et al. 2012. PubMed ID: 21562927). This variant is also reported at a maximum allele frequency of 1.7% in East Asians and 2.75% in the Finnish population and has been reported in several individuals in the homozygous state in databases of apparently unaffected individuals (http://gnomad.broadinstitute.org/variant/16-3304158-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.53	T
BayesDel_noAF	Benign	-0.52
Cadd	Benign	20
Dann	Benign	0.63
DEOGEN2	Benign	0.30	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.00076	N
LIST_S2	Benign	0.57	T
MetaRNN	Benign	0.0035	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.1	L
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-2.1	N
REVEL	Benign	0.055
Sift	Uncertain	0.0010	D
Sift4G	Benign	0.42	T
Polyphen		0.0010	B
Vest4		0.21
MutPred		0.24		Gain of solvent accessibility (P = 0.019);
MVP		0.51
MPC		0.14
ClinPred		0.0094	T
GERP RS		-1.4
Varity_R		0.16
gMVP		0.22

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.71		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.71		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs75977701; hg19: chr16-3304158; COSMIC: COSV54822200;