19-40014127-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178544.5(ZNF546):c.857A>G(p.Tyr286Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,613,212 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_178544.5 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 |
---|---|---|---|---|---|---|---|
ZNF546 | NM_178544.5 | c.857A>G | p.Tyr286Cys | missense_variant | 7/7 | ENST00000347077.9 | |
ZNF546 | NM_001297763.2 | c.779A>G | p.Tyr260Cys | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF546 | ENST00000347077.9 | c.857A>G | p.Tyr286Cys | missense_variant | 7/7 | 1 | NM_178544.5 | P2 | |
ZNF546 | ENST00000600094.5 | c.779A>G | p.Tyr260Cys | missense_variant | 7/7 | 2 | A2 | ||
ZNF546 | ENST00000596894.5 | c.77-2301A>G | intron_variant | 3 | |||||
ZNF546 | ENST00000651981.1 | c.*811A>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0000396 AC: 6AN: 151450Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251372Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135852
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461762Hom.: 0 Cov.: 35 AF XY: 0.0000220 AC XY: 16AN XY: 727166
GnomAD4 genome ? AF: 0.0000396 AC: 6AN: 151450Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73970
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.857A>G (p.Y286C) alteration is located in exon 7 (coding exon 5) of the ZNF546 gene. This alteration results from a A to G substitution at nucleotide position 857, causing the tyrosine (Y) at amino acid position 286 to be replaced by a cysteine (C). 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