chr19-2933841-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021217.3(ZNF77):c.1286C>T(p.Thr429Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,582 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 (★).
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.1286C>T | p.Thr429Met | missense_variant | 4/4 | ENST00000314531.5 | |
ZNF77 | XM_047439170.1 | c.1190C>T | p.Thr397Met | missense_variant | 4/4 | ||
ZNF77 | XM_017027081.2 | c.746C>T | p.Thr249Met | missense_variant | 3/3 | ||
ZNF77 | XM_047439171.1 | c.746C>T | p.Thr249Met | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF77 | ENST00000314531.5 | c.1286C>T | p.Thr429Met | missense_variant | 4/4 | 1 | NM_021217.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152120Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251044Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135646
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461462Hom.: 0 Cov.: 78 AF XY: 0.0000261 AC XY: 19AN XY: 726986
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.0000808 AC XY: 6AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2022 | The c.1286C>T (p.T429M) alteration is located in exon 4 (coding exon 4) of the ZNF77 gene. This alteration results from a C to T substitution at nucleotide position 1286, causing the threonine (T) at amino acid position 429 to be replaced by a methionine (M). 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