19-52613159-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018300.4(ZNF83):c.1406G>A(p.Arg469His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000856 in 1,612,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R469P) has been classified as Uncertain significance.
Frequency
Consequence
NM_018300.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF83 | NM_001105549.2 | c.1406G>A | p.Arg469His | missense_variant | Exon 6 of 6 | NP_001099019.1 | ||
ZNF83 | NM_001105550.2 | c.1406G>A | p.Arg469His | missense_variant | Exon 5 of 5 | NP_001099020.1 | ||
ZNF83 | NM_001105551.2 | c.1406G>A | p.Arg469His | missense_variant | Exon 5 of 5 | NP_001099021.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000332 AC: 5AN: 150692Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251320Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135824
GnomAD4 exome AF: 0.0000910 AC: 133AN: 1461432Hom.: 0 Cov.: 31 AF XY: 0.0000949 AC XY: 69AN XY: 726992
GnomAD4 genome AF: 0.0000332 AC: 5AN: 150692Hom.: 0 Cov.: 33 AF XY: 0.0000408 AC XY: 3AN XY: 73508
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at