chr16-71475678-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006961.4(ZNF19):c.869G>A(p.Arg290Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,612,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006961.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF19 | NM_006961.4 | c.869G>A | p.Arg290Gln | missense_variant | 6/6 | ENST00000288177.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF19 | ENST00000288177.10 | c.869G>A | p.Arg290Gln | missense_variant | 6/6 | 1 | NM_006961.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 151992Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251240Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135792
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1460334Hom.: 0 Cov.: 29 AF XY: 0.0000358 AC XY: 26AN XY: 726406
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 151992Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.869G>A (p.R290Q) alteration is located in exon 6 (coding exon 4) of the ZNF19 gene. This alteration results from a G to A substitution at nucleotide position 869, causing the arginine (R) at amino acid position 290 to be replaced by a glutamine (Q). 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