1-227654338-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001367909.1(ZNF678):āc.88A>Gā(p.Ile30Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000251 in 1,514,712 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. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001367909.1 missense, splice_region
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF678 | NM_001367909.1 | c.88A>G | p.Ile30Val | missense_variant, splice_region_variant | 4/4 | ENST00000343776.10 | NP_001354838.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF678 | ENST00000343776.10 | c.88A>G | p.Ile30Val | missense_variant, splice_region_variant | 4/4 | 1 | NM_001367909.1 | ENSP00000344828 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000484 AC: 9AN: 185952Hom.: 0 AF XY: 0.0000597 AC XY: 6AN XY: 100536
GnomAD4 exome AF: 0.0000264 AC: 36AN: 1362704Hom.: 0 Cov.: 30 AF XY: 0.0000389 AC XY: 26AN XY: 669122
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.253A>G (p.I85V) 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 253, causing the isoleucine (I) at amino acid position 85 to be replaced by a valine (V). 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