11-110137018-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033390.2(ZC3H12C):c.377T>C(p.Leu126Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000467 in 1,613,846 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_033390.2 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 |
---|---|---|---|---|---|---|---|---|---|---|
ZC3H12C | ENST00000278590.8 | c.377T>C | p.Leu126Ser | missense_variant | Exon 2 of 6 | 2 | NM_033390.2 | ENSP00000278590.3 | ||
ZC3H12C | ENST00000528673.5 | c.380T>C | p.Leu127Ser | missense_variant | Exon 2 of 6 | 2 | ENSP00000431821.1 | |||
ZC3H12C | ENST00000453089.2 | c.284T>C | p.Leu95Ser | missense_variant | Exon 1 of 5 | 2 | ENSP00000413094.2 | |||
RDX | ENST00000645527.1 | n.*251-5288A>G | intron_variant | Intron 15 of 18 | ENSP00000496121.1 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000646 AC: 160AN: 247648Hom.: 0 AF XY: 0.000603 AC XY: 81AN XY: 134412
GnomAD4 exome AF: 0.000476 AC: 696AN: 1461538Hom.: 0 Cov.: 31 AF XY: 0.000443 AC XY: 322AN XY: 727040
GnomAD4 genome AF: 0.000381 AC: 58AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.377T>C (p.L126S) alteration is located in exon 2 (coding exon 2) of the ZC3H12C gene. This alteration results from a T to C substitution at nucleotide position 377, causing the leucine (L) at amino acid position 126 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