chr19-36183619-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152477.5(ZNF565):āc.347G>Cā(p.Arg116Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152477.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF565 | NM_152477.5 | c.347G>C | p.Arg116Thr | missense_variant | 5/5 | ENST00000304116.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF565 | ENST00000304116.10 | c.347G>C | p.Arg116Thr | missense_variant | 5/5 | 2 | NM_152477.5 | P1 | |
ZNF565 | ENST00000591473.1 | c.152G>C | p.Arg51Thr | missense_variant | 4/4 | 1 | |||
ZNF565 | ENST00000355114.9 | c.467G>C | p.Arg156Thr | missense_variant | 5/5 | 2 | |||
ZNF565 | ENST00000392173.6 | c.347G>C | p.Arg116Thr | missense_variant | 5/5 | 2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251480Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135912
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727248
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.347G>C (p.R116T) alteration is located in exon 5 (coding exon 4) of the ZNF565 gene. This alteration results from a G to C substitution at nucleotide position 347, causing the arginine (R) at amino acid position 116 to be replaced by a threonine (T). 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