chr17-7461952-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001128833.2(ZBTB4):c.3030C>T(p.Gly1010=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000904 in 1,549,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000064 ( 0 hom. )
Consequence
ZBTB4
NM_001128833.2 synonymous
NM_001128833.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0570
Genes affected
ZBTB4 (HGNC:23847): (zinc finger and BTB domain containing 4) Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; methyl-CpNpG binding activity; and sequence-specific DNA binding activity. Involved in cellular response to DNA damage stimulus and negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 17-7461952-G-A is Benign according to our data. Variant chr17-7461952-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2647337.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.057 with no splicing effect.
BS2
?
High AC in GnomAd at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB4 | NM_001128833.2 | c.3030C>T | p.Gly1010= | synonymous_variant | 4/4 | ENST00000380599.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB4 | ENST00000380599.9 | c.3030C>T | p.Gly1010= | synonymous_variant | 4/4 | 1 | NM_001128833.2 | P1 | |
ZBTB4 | ENST00000311403.4 | c.3030C>T | p.Gly1010= | synonymous_variant | 4/4 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152106Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000345 AC: 7AN: 202740Hom.: 0 AF XY: 0.0000373 AC XY: 4AN XY: 107342
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GnomAD4 exome AF: 0.00000644 AC: 9AN: 1397394Hom.: 0 Cov.: 31 AF XY: 0.00000582 AC XY: 4AN XY: 687660
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GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152106Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74284
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | ZBTB4: BP4, BP7 - |
Computational scores
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Name
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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