rs79662406
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The ENST00000541159.5(MEFV):āc.1298G>Cā(p.Arg433Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R433H) has been classified as Likely benign.
Frequency
Consequence
ENST00000541159.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEFV | NM_000243.3 | c.1760-4G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000219596.6 | |||
MEFV | NM_001198536.2 | c.1298G>C | p.Arg433Pro | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEFV | ENST00000219596.6 | c.1760-4G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000243.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151958Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250940Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135714
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461664Hom.: 0 Cov.: 57 AF XY: 0.00000688 AC XY: 5AN XY: 727110
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151958Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74196
ClinVar
Submissions by phenotype
Familial Mediterranean fever Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at