17-34961594-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_052857.4(ZNF830):c.28C>T(p.Pro10Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,614,016 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P10L) has been classified as Uncertain significance.
Frequency
Consequence
NM_052857.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF830 | NM_052857.4 | c.28C>T | p.Pro10Ser | missense_variant | Exon 1 of 1 | ENST00000361952.5 | NP_443089.3 | |
CCT6B | NM_006584.4 | c.-201G>A | upstream_gene_variant | ENST00000314144.10 | NP_006575.2 | |||
CCT6B | NM_001193529.3 | c.-201G>A | upstream_gene_variant | NP_001180458.1 | ||||
CCT6B | NM_001193530.2 | c.-201G>A | upstream_gene_variant | NP_001180459.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250856Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135692
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461714Hom.: 0 Cov.: 90 AF XY: 0.00000825 AC XY: 6AN XY: 727132
GnomAD4 genome AF: 0.000197 AC: 30AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74488
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