rs224204
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000243.3(MEFV):c.1610+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,418,208 control chromosomes in the GnomAD database, including 168,563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.46 ( 16399 hom., cov: 31)
Exomes 𝑓: 0.49 ( 152164 hom. )
Consequence
MEFV
NM_000243.3 intron
NM_000243.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.212
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 16-3246429-G-A is Benign according to our data. Variant chr16-3246429-G-A is described in ClinVar as [Benign]. Clinvar id is 439879.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-3246429-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEFV | NM_000243.3 | c.1610+96C>T | intron_variant | ENST00000219596.6 | |||
MEFV | NM_001198536.2 | c.977+96C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEFV | ENST00000219596.6 | c.1610+96C>T | intron_variant | 1 | NM_000243.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.462 AC: 70117AN: 151760Hom.: 16382 Cov.: 31
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GnomAD4 exome AF: 0.487 AC: 617222AN: 1266330Hom.: 152164 Cov.: 17 AF XY: 0.484 AC XY: 309042AN XY: 638836
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GnomAD4 genome ? AF: 0.462 AC: 70171AN: 151878Hom.: 16399 Cov.: 31 AF XY: 0.467 AC XY: 34666AN XY: 74232
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 73% of patients studied by a panel of primary immunodeficiencies. Number of patients: 70. Only high quality variants are reported. - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 03, 2018 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Familial Mediterranean fever, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Familial Mediterranean fever Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at