chr19-56384707-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001320371.4(ZNF582):āc.710A>Gā(p.Asn237Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,476 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 Likely benign (ā ).
Frequency
Consequence
NM_001320371.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF582 | NM_001320371.4 | c.710A>G | p.Asn237Ser | missense_variant | 5/5 | ENST00000586929.6 | NP_001307300.2 | |
ZNF582 | NM_144690.3 | c.710A>G | p.Asn237Ser | missense_variant | 5/5 | NP_653291.1 | ||
ZNF582 | XR_007066621.1 | n.883A>G | non_coding_transcript_exon_variant | 5/6 | ||||
ZNF582 | XR_430188.4 | n.1105A>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.710A>G | p.Asn237Ser | missense_variant | 5/5 | 1 | NM_001320371.4 | ENSP00000465619 | P1 | |
ZNF582 | ENST00000301310.8 | c.710A>G | p.Asn237Ser | missense_variant | 5/5 | 1 | ENSP00000301310 | P1 | ||
ZNF582 | ENST00000589143.5 | c.232+5294A>G | intron_variant | 5 | ENSP00000468679 | |||||
ZNF582 | ENST00000589895.2 | c.232+5294A>G | intron_variant | 2 | ENSP00000465639 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249850Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135038
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460476Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726440
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at