19-57859061-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032828.4(ZNF587):c.649C>T(p.Arg217Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 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. R217H) has been classified as Uncertain significance.
Frequency
Consequence
NM_032828.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000127 AC: 19AN: 150084Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.000180 AC: 45AN: 249884Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135316
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000978 AC: 143AN: 1461492Hom.: 1 Cov.: 32 AF XY: 0.0000977 AC XY: 71AN XY: 727060
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000127 AC: 19AN: 150084Hom.: 0 Cov.: 27 AF XY: 0.0000957 AC XY: 7AN XY: 73170
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.649C>T (p.R217C) alteration is located in exon 3 (coding exon 3) of the ZNF587 gene. This alteration results from a C to T substitution at nucleotide position 649, causing the arginine (R) at amino acid position 217 to be replaced by a cysteine (C). 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