rs104895162
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_000243.3(MEFV):c.663G>C(p.Pro221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000067 in 1,612,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P221P) has been classified as Likely benign.
Frequency
Consequence
NM_000243.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEFV | NM_000243.3 | c.663G>C | p.Pro221= | synonymous_variant | 2/10 | ENST00000219596.6 | |
MEFV | NM_001198536.2 | c.277+1906G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEFV | ENST00000219596.6 | c.663G>C | p.Pro221= | synonymous_variant | 2/10 | 1 | NM_000243.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000945 AC: 23AN: 243512Hom.: 0 AF XY: 0.000120 AC XY: 16AN XY: 133116
GnomAD4 exome AF: 0.0000664 AC: 97AN: 1460564Hom.: 0 Cov.: 32 AF XY: 0.0000688 AC XY: 50AN XY: 726542
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74472
ClinVar
Submissions by phenotype
Familial Mediterranean fever Benign:1Other:1
not provided, no classification provided | literature only | Unité médicale des maladies autoinflammatoires, CHRU Montpellier | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Autoinflammatory syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Aug 18, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 15, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | MEFV: BP4, BP7 - |
MEFV-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 29, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at