16-1984230-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_005262.3(GFER):c.12C>T(p.Pro4Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,474,280 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 Likely benign (★★).
Frequency
Consequence
NM_005262.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFER | ENST00000248114.7 | c.12C>T | p.Pro4Pro | synonymous_variant | Exon 1 of 3 | 1 | NM_005262.3 | ENSP00000248114.6 | ||
GFER | ENST00000569451.1 | c.12C>T | p.Pro4Pro | synonymous_variant | Exon 1 of 2 | 5 | ENSP00000456432.1 | |||
GFER | ENST00000561710.1 | c.-28C>T | upstream_gene_variant | 2 | ENSP00000456189.1 | |||||
NOXO1 | ENST00000567471.1 | c.-392G>A | upstream_gene_variant | 5 | ENSP00000454644.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152046Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000368 AC: 3AN: 81434Hom.: 0 AF XY: 0.0000214 AC XY: 1AN XY: 46670
GnomAD4 exome AF: 0.0000129 AC: 17AN: 1322126Hom.: 0 Cov.: 32 AF XY: 0.0000184 AC XY: 12AN XY: 651854
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74400
ClinVar
Submissions by phenotype
not specified Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at