chr19-30445020-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014717.3(ZNF536):c.1458C>G(p.His486Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000261 in 1,612,124 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_014717.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF536 | NM_014717.3 | c.1458C>G | p.His486Gln | missense_variant | 2/5 | ENST00000355537.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF536 | ENST00000355537.4 | c.1458C>G | p.His486Gln | missense_variant | 2/5 | 1 | NM_014717.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000885 AC: 22AN: 248630Hom.: 0 AF XY: 0.0000815 AC XY: 11AN XY: 134896
GnomAD4 exome AF: 0.000279 AC: 408AN: 1459924Hom.: 0 Cov.: 33 AF XY: 0.000281 AC XY: 204AN XY: 726086
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.1458C>G (p.H486Q) alteration is located in exon 2 (coding exon 1) of the ZNF536 gene. This alteration results from a C to G substitution at nucleotide position 1458, causing the histidine (H) at amino acid position 486 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