19-2934126-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021217.3(ZNF77):āc.1001C>Gā(p.Thr334Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,611,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_021217.3 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 |
---|---|---|---|---|---|---|---|---|
ZNF77 | NM_021217.3 | c.1001C>G | p.Thr334Ser | missense_variant | 4/4 | ENST00000314531.5 | NP_067040.1 | |
ZNF77 | XM_047439170.1 | c.905C>G | p.Thr302Ser | missense_variant | 4/4 | |||
ZNF77 | XM_017027081.2 | c.461C>G | p.Thr154Ser | missense_variant | 3/3 | |||
ZNF77 | XM_047439171.1 | c.461C>G | p.Thr154Ser | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF77 | ENST00000314531.5 | c.1001C>G | p.Thr334Ser | missense_variant | 4/4 | 1 | NM_021217.3 | ENSP00000319053.3 |
Frequencies
GnomAD3 genomes AF: 0.00000669 AC: 1AN: 149474Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461812Hom.: 0 Cov.: 79 AF XY: 0.00000138 AC XY: 1AN XY: 727194
GnomAD4 genome AF: 0.00000669 AC: 1AN: 149474Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 72956
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 03, 2022 | The c.1001C>G (p.T334S) alteration is located in exon 4 (coding exon 4) of the ZNF77 gene. This alteration results from a C to G substitution at nucleotide position 1001, causing the threonine (T) at amino acid position 334 to be replaced by a serine (S). 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