16-3242361-CAAAAAAA-CAAAA
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_000243.3(MEFV):c.*777_*779delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000259 in 73,266 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000082 ( 0 hom., cov: 22)
Exomes 𝑓: 0.056 ( 0 hom. )
Consequence
MEFV
NM_000243.3 3_prime_UTR
NM_000243.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.338
Publications
0 publications found
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]
MEFV Gene-Disease associations (from GenCC):
- autosomal recessive familial Mediterranean feverInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- familial Mediterranean feverInheritance: AR, SD, AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Myriad Women’s Health, ClinGen, Orphanet
- familial Mediterranean fever, autosomal dominantInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000243.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MEFV | NM_000243.3 | MANE Select | c.*777_*779delTTT | 3_prime_UTR | Exon 10 of 10 | NP_000234.1 | O15553-2 | ||
| MEFV | NM_001198536.2 | c.*1327_*1329delTTT | 3_prime_UTR | Exon 9 of 9 | NP_001185465.2 | O15553-3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MEFV | ENST00000219596.6 | TSL:1 MANE Select | c.*777_*779delTTT | 3_prime_UTR | Exon 10 of 10 | ENSP00000219596.1 | O15553-2 | ||
| MEFV | ENST00000956137.1 | c.*777_*779delTTT | 3_prime_UTR | Exon 10 of 10 | ENSP00000626196.1 | ||||
| MEFV | ENST00000339854.8 | TSL:5 | c.*777_*779delTTT | 3_prime_UTR | Exon 10 of 10 | ENSP00000339639.4 | F8W6Z2 |
Frequencies
GnomAD3 genomes 0.0000822 AC: 6AN: 73032Hom.: 0 Cov.: 22 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
73032
Hom.:
Cov.:
22
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0556 AC: 13AN: 234Hom.: 0 AF XY: 0.0602 AC XY: 10AN XY: 166 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
13
AN:
234
Hom.:
AF XY:
AC XY:
10
AN XY:
166
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
0
AN:
4
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
6
South Asian (SAS)
AF:
AC:
9
AN:
134
European-Finnish (FIN)
AF:
AC:
0
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
4
AN:
82
Other (OTH)
AC:
0
AN:
0
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.287
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000822 AC: 6AN: 73032Hom.: 0 Cov.: 22 AF XY: 0.0000878 AC XY: 3AN XY: 34178 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
6
AN:
73032
Hom.:
Cov.:
22
AF XY:
AC XY:
3
AN XY:
34178
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
21022
American (AMR)
AF:
AC:
1
AN:
6098
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2102
East Asian (EAS)
AF:
AC:
0
AN:
2858
South Asian (SAS)
AF:
AC:
0
AN:
2314
European-Finnish (FIN)
AF:
AC:
3
AN:
2556
Middle Eastern (MID)
AF:
AC:
0
AN:
86
European-Non Finnish (NFE)
AF:
AC:
0
AN:
34672
Other (OTH)
AF:
AC:
0
AN:
918
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00000000481565), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.300
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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