16-3249599-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6BP7BS2_Supporting
The NM_000243.3(MEFV):c.1092G>A(p.Pro364Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,614,134 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000243.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000919 AC: 23AN: 250276Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135428
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461838Hom.: 5 Cov.: 32 AF XY: 0.0000756 AC XY: 55AN XY: 727210
GnomAD4 genome AF: 0.000309 AC: 47AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:3
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The MEFV c.1092G>A;p.Pro364Pro variant has not been described in the medical literature or in gene-specific databases. The variant is not listed in the ClinVar database, but is listed in the dbSNP variant database (rs11466022) with an allele frequency of 0.01050 percent (29/276138 alleles) in the Genome Aggregation Database. The nucleotide at this position is not well conserved across species and computational algorithms (SpliceSiteFinder-like, MaxEntScan, NNSplice, GeneSplicer, Human Splicing Finder) predict this variant is tolerated. Considering available information, this variant is classified as likely benign. -
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Familial Mediterranean fever Uncertain:1Benign:1
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Familial Mediterranean fever;C0085077:Acute febrile neutrophilic dermatosis;C1851347:Familial Mediterranean fever, autosomal dominant Benign:1
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Acute febrile neutrophilic dermatosis Benign:1
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Familial Mediterranean fever, autosomal dominant Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at