chr2-27377571-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144631.6(ZNF513):c.1600C>T(p.Arg534Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R534Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_144631.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF513 | NM_144631.6 | c.1600C>T | p.Arg534Trp | missense_variant | 4/4 | ENST00000323703.11 | |
SNX17 | NM_014748.4 | downstream_gene_variant | ENST00000233575.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF513 | ENST00000323703.11 | c.1600C>T | p.Arg534Trp | missense_variant | 4/4 | 1 | NM_144631.6 | P4 | |
ZNF513 | ENST00000407879.1 | c.1414C>T | p.Arg472Trp | missense_variant | 3/3 | 1 | A1 | ||
SNX17 | ENST00000233575.7 | downstream_gene_variant | 1 | NM_014748.4 | P1 | ||||
SNX17 | ENST00000537606.5 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250970Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135796
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461776Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727192
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 22, 2023 | This variant has not been reported in the literature in individuals affected with ZNF513-related conditions. This variant is present in population databases (rs376122709, gnomAD 0.004%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 534 of the ZNF513 protein (p.Arg534Trp). ClinVar contains an entry for this variant (Variation ID: 1040152). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at