19-40014988-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178544.5(ZNF546):c.1718G>A(p.Arg573Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,614,046 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.1718G>A | p.Arg573Gln | missense_variant | 7/7 | ENST00000347077.9 | |
ZNF546 | NM_001297763.2 | c.1640G>A | p.Arg547Gln | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF546 | ENST00000347077.9 | c.1718G>A | p.Arg573Gln | missense_variant | 7/7 | 1 | NM_178544.5 | P2 | |
ZNF546 | ENST00000600094.5 | c.1640G>A | p.Arg547Gln | missense_variant | 7/7 | 2 | A2 | ||
ZNF546 | ENST00000596894.5 | c.77-1440G>A | intron_variant | 3 | |||||
ZNF546 | ENST00000651981.1 | c.*1672G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251220Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135838
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461808Hom.: 0 Cov.: 35 AF XY: 0.0000206 AC XY: 15AN XY: 727194
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.1718G>A (p.R573Q) alteration is located in exon 7 (coding exon 5) of the ZNF546 gene. This alteration results from a G to A substitution at nucleotide position 1718, causing the arginine (R) at amino acid position 573 to be replaced by a glutamine (Q). 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