6-149451205-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207360.3(ZC3H12D):āc.1062C>Gā(p.Asp354Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000153 in 1,310,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_207360.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H12D | NM_207360.3 | c.1062C>G | p.Asp354Glu | missense_variant | 6/6 | ENST00000409806.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H12D | ENST00000409806.8 | c.1062C>G | p.Asp354Glu | missense_variant | 6/6 | 1 | NM_207360.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151996Hom.: 0 Cov.: 33
GnomAD4 exome AF: 8.64e-7 AC: 1AN: 1158030Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 553716
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151996Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.1062C>G (p.D354E) alteration is located in exon 6 (coding exon 5) of the ZC3H12D gene. This alteration results from a C to G substitution at nucleotide position 1062, causing the aspartic acid (D) at amino acid position 354 to be replaced by a glutamic acid (E). 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