11-123729668-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003455.4(ZNF202):c.560C>T(p.Pro187Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,611,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003455.4 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 |
---|---|---|---|---|---|---|---|
ZNF202 | NM_003455.4 | c.560C>T | p.Pro187Leu | missense_variant | 5/9 | ENST00000530393.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF202 | ENST00000530393.6 | c.560C>T | p.Pro187Leu | missense_variant | 5/9 | 1 | NM_003455.4 | P1 | |
ZNF202 | ENST00000336139.8 | c.560C>T | p.Pro187Leu | missense_variant | 4/8 | 1 | P1 | ||
ZNF202 | ENST00000529691.1 | c.560C>T | p.Pro187Leu | missense_variant | 3/7 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152032Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000610 AC: 15AN: 246102Hom.: 0 AF XY: 0.0000602 AC XY: 8AN XY: 132938
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1459344Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 725708
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.560C>T (p.P187L) alteration is located in exon 5 (coding exon 2) of the ZNF202 gene. This alteration results from a C to T substitution at nucleotide position 560, causing the proline (P) at amino acid position 187 to be replaced by a leucine (L). 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