chr19-52950300-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001202457.3(ZNF816):c.1475G>A(p.Arg492Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,608,344 control chromosomes in the GnomAD database, including 1 homozygotes. 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_001202457.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF816 | NM_001202457.3 | c.1475G>A | p.Arg492Gln | missense_variant | 4/4 | ENST00000444460.7 | NP_001189386.1 | |
ZNF816-ZNF321P | NM_001202473.2 | c.190+2451G>A | intron_variant | NP_001189402.1 | ||||
ZNF816 | NM_001031665.4 | c.1475G>A | p.Arg492Gln | missense_variant | 5/5 | NP_001026835.1 | ||
ZNF816 | NM_001202456.3 | c.1475G>A | p.Arg492Gln | missense_variant | 4/4 | NP_001189385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF816 | ENST00000444460.7 | c.1475G>A | p.Arg492Gln | missense_variant | 4/4 | 1 | NM_001202457.3 | ENSP00000403266 | P1 | |
ZNF816 | ENST00000357666.8 | c.1475G>A | p.Arg492Gln | missense_variant | 5/5 | 1 | ENSP00000350295 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000157 AC: 23AN: 146836Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250842Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135646
GnomAD4 exome AF: 0.000140 AC: 205AN: 1461386Hom.: 1 Cov.: 32 AF XY: 0.000147 AC XY: 107AN XY: 726984
GnomAD4 genome AF: 0.000157 AC: 23AN: 146958Hom.: 0 Cov.: 33 AF XY: 0.000125 AC XY: 9AN XY: 71718
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 16, 2021 | The c.1475G>A (p.R492Q) alteration is located in exon 5 (coding exon 3) of the ZNF816 gene. This alteration results from a G to A substitution at nucleotide position 1475, causing the arginine (R) at amino acid position 492 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