chr19-2933590-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021217.3(ZNF77):c.1537A>C(p.Thr513Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021217.3 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 |
---|---|---|---|---|---|---|---|
ZNF77 | NM_021217.3 | c.1537A>C | p.Thr513Pro | missense_variant | 4/4 | ENST00000314531.5 | |
ZNF77 | XM_047439170.1 | c.1441A>C | p.Thr481Pro | missense_variant | 4/4 | ||
ZNF77 | XM_017027081.2 | c.997A>C | p.Thr333Pro | missense_variant | 3/3 | ||
ZNF77 | XM_047439171.1 | c.997A>C | p.Thr333Pro | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF77 | ENST00000314531.5 | c.1537A>C | p.Thr513Pro | missense_variant | 4/4 | 1 | NM_021217.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461738Hom.: 0 Cov.: 77 AF XY: 0.00000275 AC XY: 2AN XY: 727130
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1537A>C (p.T513P) alteration is located in exon 4 (coding exon 4) of the ZNF77 gene. This alteration results from a A to C substitution at nucleotide position 1537, causing the threonine (T) at amino acid position 513 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