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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs28940580

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr16:3243447 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00011 (26/246254, GnomAD)
G=0.00006 (7/125568, TOPMED)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MEFV : Missense Variant
Publications
15 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 16 NC_000016.10:g.3243447C>A
GRCh38.p7 chr 16 NC_000016.10:g.3243447C>G
GRCh38.p7 chr 16 NC_000016.10:g.3243447C>T
GRCh37.p13 chr 16 NC_000016.9:g.3293447C>A
GRCh37.p13 chr 16 NC_000016.9:g.3293447C>G
GRCh37.p13 chr 16 NC_000016.9:g.3293447C>T
MEFV RefSeqGene (LRG_190) NG_007871.1:g.18181G>T
MEFV RefSeqGene (LRG_190) NG_007871.1:g.18181G>C
MEFV RefSeqGene (LRG_190) NG_007871.1:g.18181G>A
Gene: MEFV, Mediterranean fever (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MEFV transcript variant 2 NM_001198536.1:c. N/A 3 Prime UTR Variant
MEFV transcript variant 1 NM_000243.2:c.204...

NM_000243.2:c.2040G>T

M [ATG] > I [ATT] Coding Sequence Variant
pyrin isoform 1 NP_000234.1:p.Met...

NP_000234.1:p.Met680Ile

M (Met) > I (Ile) Missense Variant
MEFV transcript variant 1 NM_000243.2:c.204...

NM_000243.2:c.2040G>C

M [ATG] > I [ATC] Coding Sequence Variant
pyrin isoform 1 NP_000234.1:p.Met...

NP_000234.1:p.Met680Ile

M (Met) > I (Ile) Missense Variant
MEFV transcript variant 1 NM_000243.2:c.204...

NM_000243.2:c.2040G>A

M [ATG] > I [ATA] Coding Sequence Variant
pyrin isoform 1 NP_000234.1:p.Met...

NP_000234.1:p.Met680Ile

M (Met) > I (Ile) Missense Variant
MEFV transcript variant X1 XM_017023236.1:c....

XM_017023236.1:c.2037G>T

M [ATG] > I [ATT] Coding Sequence Variant
pyrin isoform X1 XP_016878725.1:p....

XP_016878725.1:p.Met679Ile

M (Met) > I (Ile) Missense Variant
MEFV transcript variant X1 XM_017023236.1:c....

XM_017023236.1:c.2037G>C

M [ATG] > I [ATC] Coding Sequence Variant
pyrin isoform X1 XP_016878725.1:p....

XP_016878725.1:p.Met679Ile

M (Met) > I (Ile) Missense Variant
MEFV transcript variant X1 XM_017023236.1:c....

XM_017023236.1:c.2037G>A

M [ATG] > I [ATA] Coding Sequence Variant
pyrin isoform X1 XP_016878725.1:p....

XP_016878725.1:p.Met679Ile

M (Met) > I (Ile) Missense Variant
MEFV transcript variant X2 XR_001751903.1:n. N/A Genic Downstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: A (allele ID: 231936 )
ClinVar Accession Disease Names Clinical Significance
RCV000220209.1 not provided Likely-Pathogenic
Allele: G (allele ID: 45169 )
ClinVar Accession Disease Names Clinical Significance
RCV000030179.4 Familial Mediterranean fever Pathogenic
RCV000222364.3 not provided Pathogenic
RCV000508497.1 not specified Pathogenic
RCV000515335.1 Familial Mediterranean fever,Familial mediterranean fever, autosomal dominant Pathogenic
Allele: T (allele ID: 17589 )
ClinVar Accession Disease Names Clinical Significance
RCV000002659.2 Familial Mediterranean fever Pathogenic
RCV000216518.3 not provided Pathogenic
RCV000507740.1 not specified Pathogenic
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 246254 C=0.99989 G=0.00011
The Genome Aggregation Database European Sub 134008 C=0.99982 G=0.00018
The Genome Aggregation Database Asian Sub 48030 C=1.0000 G=0.0000
The Genome Aggregation Database American Sub 33578 C=1.0000 G=0.0000
The Genome Aggregation Database African Sub 15304 C=1.0000 G=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 C=1.000 G=0.000
The Genome Aggregation Database Other Sub 5484 C=1.000 G=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99993 T=0.00002, G=0.00006
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= A G T Note
GRCh38.p7 chr 16 NC_000016.10:...

NC_000016.10:g.3243447C=

NC_000016.10:...

NC_000016.10:g.3243447C>A

NC_000016.10:...

NC_000016.10:g.3243447C>G

NC_000016.10:...

NC_000016.10:g.3243447C>T

GRCh37.p13 chr 16 NC_000016.9:g...

NC_000016.9:g.3293447C=

NC_000016.9:g...

NC_000016.9:g.3293447C>A

NC_000016.9:g...

NC_000016.9:g.3293447C>G

NC_000016.9:g...

NC_000016.9:g.3293447C>T

MEFV RefSeqGene (LRG_190) NG_007871.1:g...

NG_007871.1:g.18181G=

NG_007871.1:g...

NG_007871.1:g.18181G>T

NG_007871.1:g...

NG_007871.1:g.18181G>C

NG_007871.1:g...

NG_007871.1:g.18181G>A

MEFV transcript variant 1 NM_000243.2:c...

NM_000243.2:c.2040G=

NM_000243.2:c...

NM_000243.2:c.2040G>T

NM_000243.2:c...

NM_000243.2:c.2040G>C

NM_000243.2:c...

NM_000243.2:c.2040G>A

MEFV transcript variant 2 NM_001198536....

NM_001198536.1:c.*244G=

NM_001198536....

NM_001198536.1:c.*244G>T

NM_001198536....

NM_001198536.1:c.*244G>C

NM_001198536....

NM_001198536.1:c.*244G>A

MEFV transcript variant X1 XM_017023236....

XM_017023236.1:c.2037G=

XM_017023236....

XM_017023236.1:c.2037G>T

XM_017023236....

XM_017023236.1:c.2037G>C

XM_017023236....

XM_017023236.1:c.2037G>A

pyrin isoform 1 NP_000234.1:p...

NP_000234.1:p.Met680=

NP_000234.1:p...

NP_000234.1:p.Met680Ile

NP_000234.1:p...

NP_000234.1:p.Met680Ile

NP_000234.1:p...

NP_000234.1:p.Met680Ile

pyrin isoform X1 XP_016878725....

XP_016878725.1:p.Met679=

XP_016878725....

XP_016878725.1:p.Met679Ile

XP_016878725....

XP_016878725.1:p.Met679Ile

XP_016878725....

XP_016878725.1:p.Met679Ile

Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

2 Frequency, 13 SubSNP, 8 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CORRELAGEN ss472343190 Nov 18, 2011 (136)
2 NCBI-CURATED-RECORDS ss537713863 Jan 04, 2013 (137)
3 NCBI-CURATED-RECORDS ss537713866 Jan 04, 2013 (137)
4 NHLBI-ESP ss713280264 Apr 25, 2013 (138)
5 EVA_EXAC ss1692116118 Apr 01, 2015 (144)
6 EVA_EXAC ss1692116119 Apr 01, 2015 (144)
7 CLINVAR ss2137494081 Feb 03, 2017 (149)
8 HUMAN_LONGEVITY ss2210009861 Dec 20, 2016 (150)
9 TOPMED ss2374622639 Dec 20, 2016 (150)
10 GNOMAD ss2741692179 Nov 08, 2017 (151)
11 AFFY ss2985057408 Nov 08, 2017 (151)
12 TOPMED ss3238148679 Nov 08, 2017 (151)
13 TOPMED ss3238148680 Nov 08, 2017 (151)
14 The Genome Aggregation Database NC_000016.9 - 3293447 Jul 20, 2018 (151)
15 Trans-Omics for Precision Medicine NC_000016.10 - 3243447 Jul 20, 2018 (151)
16 ClinVar RCV000002659.2 Jul 20, 2018 (151)
17 ClinVar RCV000030179.4 Jul 20, 2018 (151)
18 ClinVar RCV000216518.3 Jul 20, 2018 (151)
19 ClinVar RCV000220209.1 Jul 20, 2018 (151)
20 ClinVar RCV000222364.3 Jul 20, 2018 (151)
21 ClinVar RCV000507740.1 Jul 20, 2018 (151)
22 ClinVar RCV000508497.1 Jul 20, 2018 (151)
23 ClinVar RCV000515335.1 Jul 20, 2018 (151)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
10706914, ss713280264, ss1692116118, ss1692116119, ss2374622639, ss2741692179, ss2985057408 NC_000016.9:3293446:C= NC_000016.10:3243446:C= (self)
138052170, ss472343190, ss537713863, ss537713866, ss2137494081, ss2210009861, ss3238148679, ss3238148680 NC_000016.10:3243446:C= NC_000016.10:3243446:C= (self)
RCV000220209.1, ss2137494081 NC_000016.10:3243446:C>A NC_000016.10:3243446:C>A (self)
10706914, ss713280264, ss1692116118, ss2741692179, ss2985057408 NC_000016.9:3293446:C>G NC_000016.10:3243446:C>G (self)
RCV000030179.4, RCV000222364.3, RCV000508497.1, RCV000515335.1, 138052170, ss472343190, ss537713866, ss2210009861, ss3238148679 NC_000016.10:3243446:C>G NC_000016.10:3243446:C>G (self)
ss1692116119, ss2374622639 NC_000016.9:3293446:C>T NC_000016.10:3243446:C>T (self)
RCV000002659.2, RCV000216518.3, RCV000507740.1, 138052170, ss537713863, ss3238148680 NC_000016.10:3243446:C>T NC_000016.10:3243446:C>T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

15 citations for rs28940580
PMID Title Author Year Journal
12401 [X-ray assessment of the motor-evacuatory function of the gastrointestinal tract in the diagnosis of the dumping-syndrome]. Fil'shtinskiĭ AIa et al. 1976 Klinicheskaia khirurgiia
9288094 A candidate gene for familial Mediterranean fever. French FMF Consortium. et al. 1997 Nature genetics
9288758 Ancient missense mutations in a new member of the RoRet gene family are likely to cause familial Mediterranean fever. The International FMF Consortium. 1997 Cell
10024914 Pyrin/marenostrin mutations in familial Mediterranean fever. Booth DR et al. 1998 QJM
10090880 Mutation and haplotype studies of familial Mediterranean fever reveal new ancestral relationships and evidence for a high carrier frequency with reduced penetrance in the Ashkenazi Jewish population. Aksentijevich I et al. 1999 American journal of human genetics
10447272 Direct detection of common mutations in the familial Mediterranean fever gene (MEFV) using naturally occurring and primer mediated restriction fragment analysis. Mutation in brief no. 257. Online. Gershoni-Baruch R et al. 1999 Human mutation
10737995 The E148Q mutation in the MEFV gene: is it a disease-causing mutation or a sequence variant? Ben-Chetrit E et al. 2000 Human mutation
11017802 Identification of MEFV-independent modifying genetic factors for familial Mediterranean fever. Cazeneuve C et al. 2000 American journal of human genetics
12105243 Mutational spectrum in the MEFV and TNFRSF1A genes in patients suffering from AA amyloidosis and recurrent inflammatory attacks. Dodé C et al. 2002 Nephrology, dialysis, transplantation
16439335 Prevalence and distribution of MEFV mutations among Arabs from the Maghreb patients suffering from familial Mediterranean fever. Belmahi L et al. 2006 Comptes rendus biologies
19784369 Genetic variation in the familial Mediterranean fever gene (MEFV) and risk for Crohn's disease and ulcerative colitis. Villani AC et al. 2009 PloS one
25866490 Genetic profiling of autoinflammatory disorders in patients with periodic fever: a prospective study. De Pieri C et al. 2015 Pediatric rheumatology online journal
26839472 Clinical and Genetic Features of Korean Patients with Recurrent Fever and Multi-System Inflammation without Infectious or Autoimmune Evidence. Yang JA et al. 2016 Journal of Korean medical science
27621632 Association between sequence variations of the Mediterranean fever gene and the risk of migraine: a case-control study. Coşkun S et al. 2016 Neuropsychiatric disease and treatment
27796522 The association between MEFV gene polymorphisms and Henoch-Schönlein purpura, and additional SNP-SNP interactions in Chinese Han children. Xiong S et al. 2017 Rheumatology international

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e