chr19-58562737-C-G
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_198055.2(MZF1):c.1540G>C(p.Gly514Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000348 in 1,536,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198055.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MZF1 | NM_198055.2 | c.1540G>C | p.Gly514Arg | missense_variant | Exon 6 of 6 | ENST00000215057.7 | NP_932172.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152124Hom.: 0 Cov.: 34 show subpopulations
GnomAD2 exomes AF: 0.000280 AC: 37AN: 131994 AF XY: 0.000290 show subpopulations
GnomAD4 exome AF: 0.000367 AC: 508AN: 1383980Hom.: 0 Cov.: 31 AF XY: 0.000369 AC XY: 252AN XY: 683206 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000171 AC: 26AN: 152242Hom.: 0 Cov.: 34 AF XY: 0.000161 AC XY: 12AN XY: 74438 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1540G>C (p.G514R) alteration is located in exon 6 (coding exon 5) of the MZF1 gene. This alteration results from a G to C substitution at nucleotide position 1540, causing the glycine (G) at amino acid position 514 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at