19-37128363-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144689.5(ZNF420):c.1372C>T(p.Arg458Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,982 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_144689.5 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 | UniProt |
---|---|---|---|---|---|---|---|
ZNF420 | NM_144689.5 | c.1372C>T | p.Arg458Cys | missense_variant | 5/5 | ENST00000337995.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF420 | ENST00000337995.4 | c.1372C>T | p.Arg458Cys | missense_variant | 5/5 | 1 | NM_144689.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152106Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251124Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135706
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461758Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727162
GnomAD4 genome AF: 0.000112 AC: 17AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1372C>T (p.R458C) alteration is located in exon 5 (coding exon 3) of the ZNF420 gene. This alteration results from a C to T substitution at nucleotide position 1372, causing the arginine (R) at amino acid position 458 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