chr19-52950552-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.1223G>A(p.Arg408His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,528 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_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.1223G>A | p.Arg408His | missense_variant | 4/4 | ENST00000444460.7 | NP_001189386.1 | |
ZNF816-ZNF321P | NM_001202473.2 | c.190+2199G>A | intron_variant | NP_001189402.1 | ||||
ZNF816 | NM_001031665.4 | c.1223G>A | p.Arg408His | missense_variant | 5/5 | NP_001026835.1 | ||
ZNF816 | NM_001202456.3 | c.1223G>A | p.Arg408His | missense_variant | 4/4 | NP_001189385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF816 | ENST00000444460.7 | c.1223G>A | p.Arg408His | missense_variant | 4/4 | 1 | NM_001202457.3 | ENSP00000403266 | P1 | |
ZNF816 | ENST00000357666.8 | c.1223G>A | p.Arg408His | missense_variant | 5/5 | 1 | ENSP00000350295 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 151938Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251376Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135874
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461472Hom.: 0 Cov.: 66 AF XY: 0.0000330 AC XY: 24AN XY: 727052
GnomAD4 genome AF: 0.000105 AC: 16AN: 152056Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.1223G>A (p.R408H) 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 1223, causing the arginine (R) at amino acid position 408 to be replaced by a histidine (H). 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