19-37127812-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.821C>T(p.Thr274Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF420 | ENST00000337995.4 | c.821C>T | p.Thr274Ile | missense_variant | Exon 5 of 5 | 1 | NM_144689.5 | ENSP00000338770.2 | ||
ENSG00000267360 | ENST00000588873.1 | c.253+28053G>A | intron_variant | Intron 3 of 3 | 5 | ENSP00000465212.1 |
Frequencies
GnomAD3 genomes AF: 0.000546 AC: 83AN: 151986Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250712Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135644
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461748Hom.: 0 Cov.: 32 AF XY: 0.0000591 AC XY: 43AN XY: 727168
GnomAD4 genome AF: 0.000546 AC: 83AN: 152104Hom.: 0 Cov.: 33 AF XY: 0.000538 AC XY: 40AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.821C>T (p.T274I) 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 821, causing the threonine (T) at amino acid position 274 to be replaced by an isoleucine (I). 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