chr19-47066961-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015168.2(ZC3H4):c.3307C>T(p.Pro1103Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,593,364 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015168.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H4 | NM_015168.2 | c.3307C>T | p.Pro1103Ser | missense_variant | 15/15 | ENST00000253048.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H4 | ENST00000253048.10 | c.3307C>T | p.Pro1103Ser | missense_variant | 15/15 | 1 | NM_015168.2 | P1 | |
ZC3H4 | ENST00000601973.1 | c.2128C>T | p.Pro710Ser | missense_variant | 8/8 | 5 | |||
ZC3H4 | ENST00000594019.5 | n.1157C>T | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000290 AC: 63AN: 217350Hom.: 0 AF XY: 0.000200 AC XY: 24AN XY: 120036
GnomAD4 exome AF: 0.0000513 AC: 74AN: 1441158Hom.: 0 Cov.: 33 AF XY: 0.0000406 AC XY: 29AN XY: 714988
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
ZC3H4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at