rs142860188
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_015100.4(POGZ):āc.4089T>Gā(p.His1363Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,614,140 control chromosomes in the GnomAD database, including 6 homozygotes. 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 ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H1363R) has been classified as Likely benign.
Frequency
Consequence
NM_015100.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POGZ | NM_015100.4 | c.4089T>G | p.His1363Gln | missense_variant | 19/19 | ENST00000271715.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POGZ | ENST00000271715.7 | c.4089T>G | p.His1363Gln | missense_variant | 19/19 | 1 | NM_015100.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00112 AC: 170AN: 152140Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00132 AC: 331AN: 251476Hom.: 0 AF XY: 0.00152 AC XY: 206AN XY: 135916
GnomAD4 exome AF: 0.00129 AC: 1893AN: 1461882Hom.: 5 Cov.: 36 AF XY: 0.00140 AC XY: 1018AN XY: 727242
GnomAD4 genome ? AF: 0.00112 AC: 170AN: 152258Hom.: 1 Cov.: 32 AF XY: 0.00101 AC XY: 75AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 03, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | POGZ: BP4, BS1 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 24, 2019 | This variant is associated with the following publications: (PMID: 26942287, 26739615) - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2018 | 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. - |
POGZ-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 21, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Autism spectrum disorder Other:1
association, no assertion criteria provided | clinical testing | Center of Medical Genetics, Central South University | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at