chr2-184937190-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_194250.2(ZNF804A):āc.1794A>Gā(p.Lys598=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,595,064 control chromosomes in the GnomAD database, including 33,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.15 ( 2259 hom., cov: 33)
Exomes š: 0.20 ( 30930 hom. )
Consequence
ZNF804A
NM_194250.2 synonymous
NM_194250.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.00
Genes affected
ZNF804A (HGNC:21711): (zinc finger protein 804A) The protein encoded by this gene is a zinc finger binding protein. Polymorphisms in this gene, especially rs1344706, are thought to confer increased susceptibility to schizophrenia, bipolar disorder, and heroin addiciton. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 2-184937190-A-G is Benign according to our data. Variant chr2-184937190-A-G is described in ClinVar as [Benign]. Clinvar id is 3060253.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=2 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF804A | NM_194250.2 | c.1794A>G | p.Lys598= | synonymous_variant | 4/4 | ENST00000302277.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF804A | ENST00000302277.7 | c.1794A>G | p.Lys598= | synonymous_variant | 4/4 | 1 | NM_194250.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.153 AC: 23262AN: 152064Hom.: 2256 Cov.: 33
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GnomAD3 exomes AF: 0.197 AC: 45328AN: 230060Hom.: 5072 AF XY: 0.206 AC XY: 25895AN XY: 125492
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GnomAD4 exome AF: 0.201 AC: 290554AN: 1442882Hom.: 30930 Cov.: 47 AF XY: 0.205 AC XY: 146779AN XY: 717646
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GnomAD4 genome AF: 0.153 AC: 23257AN: 152182Hom.: 2259 Cov.: 33 AF XY: 0.153 AC XY: 11406AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ZNF804A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 12, 2019 | 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). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at