19-47066568-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015168.2(ZC3H4):c.3700G>A(p.Ala1234Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000319 in 1,569,532 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.3700G>A | p.Ala1234Thr | missense_variant | 15/15 | ENST00000253048.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H4 | ENST00000253048.10 | c.3700G>A | p.Ala1234Thr | missense_variant | 15/15 | 1 | NM_015168.2 | P1 | |
ZC3H4 | ENST00000601973.1 | c.2521G>A | p.Ala841Thr | missense_variant | 8/8 | 5 | |||
ZC3H4 | ENST00000594019.5 | n.1550G>A | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000662 AC: 1AN: 150950Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 5AN: 206562Hom.: 0 AF XY: 0.00000887 AC XY: 1AN XY: 112710
GnomAD4 exome AF: 0.0000345 AC: 49AN: 1418582Hom.: 0 Cov.: 32 AF XY: 0.0000299 AC XY: 21AN XY: 701236
GnomAD4 genome ? AF: 0.00000662 AC: 1AN: 150950Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 73756
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.3700G>A (p.A1234T) 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 3700, causing the alanine (A) at amino acid position 1234 to be replaced by a threonine (T). 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