19-47066643-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015168.2(ZC3H4):c.3625G>A(p.Gly1209Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,611,846 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 Uncertain significance (★).
Frequency
Consequence
NM_015168.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H4 | NM_015168.2 | c.3625G>A | p.Gly1209Ser | missense_variant | 15/15 | ENST00000253048.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H4 | ENST00000253048.10 | c.3625G>A | p.Gly1209Ser | missense_variant | 15/15 | 1 | NM_015168.2 | P1 | |
ZC3H4 | ENST00000601973.1 | c.2446G>A | p.Gly816Ser | missense_variant | 8/8 | 5 | |||
ZC3H4 | ENST00000594019.5 | n.1475G>A | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 239210Hom.: 0 AF XY: 0.00000761 AC XY: 1AN XY: 131354
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459632Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 6AN XY: 726066
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.3625G>A (p.G1209S) alteration is located in exon 15 (coding exon 14) of the ZC3H4 gene. This alteration results from a G to A substitution at nucleotide position 3625, causing the glycine (G) at amino acid position 1209 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