9-111530912-G-A
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_133464.5(ZNF483):c.450G>A(p.Glu150Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000969 in 1,548,304 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_133464.5 synonymous
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF483 | ENST00000309235.6 | c.450G>A | p.Glu150Glu | synonymous_variant | Exon 3 of 6 | 1 | NM_133464.5 | ENSP00000311679.5 | ||
ZNF483 | ENST00000355824.7 | c.450G>A | p.Glu150Glu | synonymous_variant | Exon 3 of 6 | 1 | ENSP00000438048.1 | |||
ZNF483 | ENST00000358151.8 | c.450G>A | p.Glu150Glu | synonymous_variant | Exon 3 of 6 | 2 | ENSP00000350871.4 |
Frequencies
GnomAD3 genomes AF: 0.0000732 AC: 11AN: 150212Hom.: 0 Cov.: 26 show subpopulations
GnomAD2 exomes AF: 0.0000695 AC: 17AN: 244718 AF XY: 0.0000680 show subpopulations
GnomAD4 exome AF: 0.0000994 AC: 139AN: 1397982Hom.: 0 Cov.: 28 AF XY: 0.000105 AC XY: 73AN XY: 695934 show subpopulations
GnomAD4 genome AF: 0.0000732 AC: 11AN: 150322Hom.: 0 Cov.: 26 AF XY: 0.0000818 AC XY: 6AN XY: 73386 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at