chr20-63961404-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020713.3(ZNF512B):c.2332G>T(p.Ala778Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000209 in 1,611,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A778V) has been classified as Uncertain significance.
Frequency
Consequence
NM_020713.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF512B | NM_020713.3 | c.2332G>T | p.Ala778Ser | missense_variant | 16/17 | ENST00000369888.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF512B | ENST00000369888.6 | c.2332G>T | p.Ala778Ser | missense_variant | 16/17 | 1 | NM_020713.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00108 AC: 165AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000337 AC: 84AN: 248894Hom.: 0 AF XY: 0.000252 AC XY: 34AN XY: 134914
GnomAD4 exome AF: 0.000117 AC: 171AN: 1459016Hom.: 0 Cov.: 31 AF XY: 0.000110 AC XY: 80AN XY: 725886
GnomAD4 genome ? AF: 0.00108 AC: 165AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74484
ClinVar
Submissions by phenotype
ZNF512B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 17, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at