19-52613159-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001277948.2(ZNF83):āc.1406G>Cā(p.Arg469Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,612,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001277948.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF83 | NM_018300.4 | c.1406G>C | p.Arg469Pro | missense_variant | 3/3 | ENST00000301096.8 | |
ZNF83 | NM_001277948.2 | c.1406G>C | p.Arg469Pro | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF83 | ENST00000301096.8 | c.1406G>C | p.Arg469Pro | missense_variant | 3/3 | 3 | NM_018300.4 | P1 | |
ENST00000702778.1 | n.82-7940C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000146 AC: 22AN: 150692Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251320Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135824
GnomAD4 exome AF: 0.000155 AC: 226AN: 1461432Hom.: 0 Cov.: 31 AF XY: 0.000146 AC XY: 106AN XY: 726992
GnomAD4 genome AF: 0.000146 AC: 22AN: 150692Hom.: 0 Cov.: 33 AF XY: 0.000122 AC XY: 9AN XY: 73508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 21, 2024 | The c.1406G>C (p.R469P) alteration is located in exon 6 (coding exon 1) of the ZNF83 gene. This alteration results from a G to C substitution at nucleotide position 1406, causing the arginine (R) at amino acid position 469 to be replaced by a proline (P). 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