chr19-56383939-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001320371.4(ZNF582):c.1478C>T(p.Pro493Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,450 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 Uncertain significance (★).
Frequency
Consequence
NM_001320371.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF582 | NM_001320371.4 | c.1478C>T | p.Pro493Leu | missense_variant | 5/5 | ENST00000586929.6 | NP_001307300.2 | |
ZNF582 | NM_144690.3 | c.1478C>T | p.Pro493Leu | missense_variant | 5/5 | NP_653291.1 | ||
ZNF582 | XR_007066621.1 | n.1651C>T | non_coding_transcript_exon_variant | 5/6 | ||||
ZNF582 | XR_430188.4 | n.1873C>T | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF582 | ENST00000586929.6 | c.1478C>T | p.Pro493Leu | missense_variant | 5/5 | 1 | NM_001320371.4 | ENSP00000465619 | P1 | |
ENST00000651165.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460450Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726460
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.1478C>T (p.P493L) alteration is located in exon 5 (coding exon 4) of the ZNF582 gene. This alteration results from a C to T substitution at nucleotide position 1478, causing the proline (P) at amino acid position 493 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