19-47066697-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015168.2(ZC3H4):c.3571G>A(p.Val1191Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000994 in 1,609,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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
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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.3571G>A | p.Val1191Ile | missense_variant | 15/15 | ENST00000253048.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H4 | ENST00000253048.10 | c.3571G>A | p.Val1191Ile | missense_variant | 15/15 | 1 | NM_015168.2 | P1 | |
ZC3H4 | ENST00000601973.1 | c.2392G>A | p.Val798Ile | missense_variant | 8/8 | 5 | |||
ZC3H4 | ENST00000594019.5 | n.1421G>A | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 234938Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 129052
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1457384Hom.: 0 Cov.: 33 AF XY: 0.00000828 AC XY: 6AN XY: 724760
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.3571G>A (p.V1191I) 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 3571, causing the valine (V) at amino acid position 1191 to be replaced by an isoleucine (I). 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