chr12-133048690-A-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001289971.2(ZNF84):c.143-63A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 1,296,676 control chromosomes in the GnomAD database, including 123,045 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.46 ( 16879 hom., cov: 32)
Exomes 𝑓: 0.43 ( 106166 hom. )
Consequence
ZNF84
NM_001289971.2 intron
NM_001289971.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.858
Genes affected
ZNF84 (HGNC:13159): (zinc finger protein 84) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.92).
BP6
Variant 12-133048690-A-T is Benign according to our data. Variant chr12-133048690-A-T is described in ClinVar as [Benign]. Clinvar id is 982074.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.460 AC: 69907AN: 151844Hom.: 16869 Cov.: 32
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GnomAD4 exome AF: 0.426 AC: 487268AN: 1144716Hom.: 106166 Cov.: 14 AF XY: 0.427 AC XY: 247702AN XY: 580166
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GnomAD4 genome AF: 0.460 AC: 69944AN: 151960Hom.: 16879 Cov.: 32 AF XY: 0.455 AC XY: 33823AN XY: 74258
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
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Pathology and Clinical Laboratory Medicine, King Fahad Medical City
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at