chr19-56384165-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001320371.4(ZNF582):āc.1252A>Gā(p.Thr418Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,460,130 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 (ā ).
Frequency
Consequence
NM_001320371.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF582 | NM_001320371.4 | c.1252A>G | p.Thr418Ala | missense_variant | 5/5 | ENST00000586929.6 | NP_001307300.2 | |
ZNF582 | NM_144690.3 | c.1252A>G | p.Thr418Ala | missense_variant | 5/5 | NP_653291.1 | ||
ZNF582 | XR_007066621.1 | n.1425A>G | non_coding_transcript_exon_variant | 5/6 | ||||
ZNF582 | XR_430188.4 | n.1647A>G | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF582 | ENST00000586929.6 | c.1252A>G | p.Thr418Ala | missense_variant | 5/5 | 1 | NM_001320371.4 | ENSP00000465619 | P1 | |
ZNF582 | ENST00000301310.8 | c.1252A>G | p.Thr418Ala | missense_variant | 5/5 | 1 | ENSP00000301310 | P1 | ||
ZNF582 | ENST00000589143.5 | c.232+5836A>G | intron_variant | 5 | ENSP00000468679 | |||||
ZNF582 | ENST00000589895.2 | c.232+5836A>G | intron_variant | 2 | ENSP00000465639 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249348Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134776
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460130Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726252
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.1252A>G (p.T418A) alteration is located in exon 5 (coding exon 4) of the ZNF582 gene. This alteration results from a A to G substitution at nucleotide position 1252, causing the threonine (T) at amino acid position 418 to be replaced by an alanine (A). 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