6-151365770-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_020861.3(ZBTB2):c.1296G>A(p.Glu432Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 1,613,910 control chromosomes in the GnomAD database, including 295,435 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.54 ( 23512 hom., cov: 32)
Exomes 𝑓: 0.60 ( 271923 hom. )
Consequence
ZBTB2
NM_020861.3 synonymous
NM_020861.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.458
Genes affected
ZBTB2 (HGNC:20868): (zinc finger and BTB domain containing 2) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 6-151365770-C-T is Benign according to our data. Variant chr6-151365770-C-T is described in ClinVar as [Benign]. Clinvar id is 1286394.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.458 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.541 AC: 82180AN: 151934Hom.: 23510 Cov.: 32
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GnomAD3 exomes AF: 0.554 AC: 139177AN: 251332Hom.: 40667 AF XY: 0.549 AC XY: 74589AN XY: 135840
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GnomAD4 exome AF: 0.603 AC: 881746AN: 1461858Hom.: 271923 Cov.: 80 AF XY: 0.597 AC XY: 434157AN XY: 727224
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GnomAD4 genome AF: 0.541 AC: 82216AN: 152052Hom.: 23512 Cov.: 32 AF XY: 0.538 AC XY: 39991AN XY: 74314
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 15, 2020
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at