chr16-3244246-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000243.3(MEFV):c.1759+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00377 in 1,613,954 control chromosomes in the GnomAD database, including 270 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000243.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEFV | NM_000243.3 | c.1759+8C>T | splice_region_variant, intron_variant | Intron 8 of 9 | ENST00000219596.6 | NP_000234.1 | ||
MEFV | NM_001198536.2 | c.1126+8C>T | splice_region_variant, intron_variant | Intron 7 of 8 | NP_001185465.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00463 AC: 703AN: 151990Hom.: 26 Cov.: 32
GnomAD3 exomes AF: 0.00930 AC: 2337AN: 251346Hom.: 124 AF XY: 0.00935 AC XY: 1270AN XY: 135834
GnomAD4 exome AF: 0.00368 AC: 5377AN: 1461846Hom.: 245 Cov.: 36 AF XY: 0.00391 AC XY: 2843AN XY: 727218
GnomAD4 genome AF: 0.00462 AC: 702AN: 152108Hom.: 25 Cov.: 32 AF XY: 0.00523 AC XY: 389AN XY: 74356
ClinVar
Submissions by phenotype
Familial Mediterranean fever Benign:5Other:1
- -
- -
- -
- -
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
- -
not specified Benign:2
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. -
- -
Acute febrile neutrophilic dermatosis Benign:1
- -
not provided Benign:1
- -
Familial Mediterranean fever, autosomal dominant Benign:1
- -
Autoinflammatory syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at