20-297761-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033089.7(ZCCHC3):c.175C>T(p.Pro59Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000733 in 1,378,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033089.7 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZCCHC3 | NM_033089.7 | c.175C>T | p.Pro59Ser | missense_variant | 1/1 | ENST00000500893.4 | NP_149080.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZCCHC3 | ENST00000500893.4 | c.175C>T | p.Pro59Ser | missense_variant | 1/1 | NM_033089.7 | ENSP00000484056 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000199 AC: 3AN: 150632Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000798 AC: 98AN: 1228038Hom.: 0 Cov.: 32 AF XY: 0.0000732 AC XY: 44AN XY: 601476
GnomAD4 genome AF: 0.0000199 AC: 3AN: 150632Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73584
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.175C>T (p.P59S) alteration is located in exon 1 (coding exon 1) of the ZCCHC3 gene. This alteration results from a C to T substitution at nucleotide position 175, causing the proline (P) at amino acid position 59 to be replaced by a serine (S). 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