19-21536556-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001415.4(ZNF429):c.503C>T(p.Thr168Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T168N) has been classified as Likely benign.
Frequency
Consequence
NM_001001415.4 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 |
---|---|---|---|---|---|---|---|
ZNF429 | NM_001001415.4 | c.503C>T | p.Thr168Ile | missense_variant | 4/4 | ENST00000358491.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF429 | ENST00000358491.9 | c.503C>T | p.Thr168Ile | missense_variant | 4/4 | 3 | NM_001001415.4 | P1 | |
ZNF429 | ENST00000597078.5 | c.227-5208C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 249884Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135466
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461274Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726956
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.503C>T (p.T168I) alteration is located in exon 4 (coding exon 4) of the ZNF429 gene. This alteration results from a C to T substitution at nucleotide position 503, causing the threonine (T) at amino acid position 168 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