19-57858879-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_032828.4(ZNF587):c.467C>T(p.Ser156Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF587 | ENST00000339656.8 | c.467C>T | p.Ser156Leu | missense_variant | Exon 3 of 3 | 1 | NM_032828.4 | ENSP00000345479.4 | ||
ENSG00000268750 | ENST00000593873.6 | c.*109C>T | 3_prime_UTR_variant | Exon 2 of 2 | 4 | ENSP00000469133.2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 8AN: 148488Hom.: 0 Cov.: 26 FAILED QC
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243374Hom.: 0 AF XY: 0.00000757 AC XY: 1AN XY: 132176
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000411 AC: 6AN: 1460820Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726746
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000539 AC: 8AN: 148488Hom.: 0 Cov.: 26 AF XY: 0.0000554 AC XY: 4AN XY: 72234
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.467C>T (p.S156L) 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 467, causing the serine (S) at amino acid position 156 to be replaced by a leucine (L). 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