chr1-227654888-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001367909.1(ZNF678):c.638A>G(p.Glu213Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,608,670 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 (★).
Frequency
Consequence
NM_001367909.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF678 | NM_001367909.1 | c.638A>G | p.Glu213Gly | missense_variant | 4/4 | ENST00000343776.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF678 | ENST00000343776.10 | c.638A>G | p.Glu213Gly | missense_variant | 4/4 | 1 | NM_001367909.1 | P1 | |
ZNF678 | ENST00000397097.4 | c.638A>G | p.Glu213Gly | missense_variant | 2/2 | 1 | P1 | ||
ZNF678 | ENST00000608949.5 | c.226+412A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000330 AC: 5AN: 151336Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000565 AC: 14AN: 247970Hom.: 0 AF XY: 0.0000521 AC XY: 7AN XY: 134264
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1457334Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 724996
GnomAD4 genome ? AF: 0.0000330 AC: 5AN: 151336Hom.: 0 Cov.: 33 AF XY: 0.0000271 AC XY: 2AN XY: 73914
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.803A>G (p.E268G) alteration is located in exon 4 (coding exon 4) of the ZNF678 gene. This alteration results from a A to G substitution at nucleotide position 803, causing the glutamic acid (E) at amino acid position 268 to be replaced by a glycine (G). 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