9-96819548-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001662.3(ZNF782):c.475A>G(p.Lys159Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,612,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001662.3 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 |
---|---|---|---|---|---|---|---|
ZNF782 | NM_001001662.3 | c.475A>G | p.Lys159Glu | missense_variant | 6/6 | ENST00000481138.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF782 | ENST00000481138.6 | c.475A>G | p.Lys159Glu | missense_variant | 6/6 | 1 | NM_001001662.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249802Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134970
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460368Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 726374
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.475A>G (p.K159E) alteration is located in exon 6 (coding exon 4) of the ZNF782 gene. This alteration results from a A to G substitution at nucleotide position 475, causing the lysine (K) at amino acid position 159 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