chr19-56383975-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001320371.4(ZNF582):āc.1442T>Cā(p.Ile481Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,613,914 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 (ā ).
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.1442T>C | p.Ile481Thr | missense_variant | 5/5 | ENST00000586929.6 | NP_001307300.2 | |
ZNF582 | NM_144690.3 | c.1442T>C | p.Ile481Thr | missense_variant | 5/5 | NP_653291.1 | ||
ZNF582 | XR_007066621.1 | n.1615T>C | non_coding_transcript_exon_variant | 5/6 | ||||
ZNF582 | XR_430188.4 | n.1837T>C | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF582 | ENST00000586929.6 | c.1442T>C | p.Ile481Thr | missense_variant | 5/5 | 1 | NM_001320371.4 | ENSP00000465619 | P1 | |
ZNF582 | ENST00000301310.8 | c.1442T>C | p.Ile481Thr | missense_variant | 5/5 | 1 | ENSP00000301310 | P1 | ||
ZNF582 | ENST00000589143.5 | c.232+6026T>C | intron_variant | 5 | ENSP00000468679 | |||||
ZNF582 | ENST00000589895.2 | c.232+6026T>C | intron_variant | 2 | ENSP00000465639 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251066Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135694
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461594Hom.: 0 Cov.: 31 AF XY: 0.000186 AC XY: 135AN XY: 727070
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 20, 2023 | The c.1442T>C (p.I481T) alteration is located in exon 5 (coding exon 4) of the ZNF582 gene. This alteration results from a T to C substitution at nucleotide position 1442, causing the isoleucine (I) at amino acid position 481 to be replaced by a threonine (T). 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