chr1-15944172-CTGGGTGAACAAGCTGA-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_003443.3(ZBTB17):c.1371+112_1371+127del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,375,848 control chromosomes in the GnomAD database, including 513 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.034 ( 282 hom., cov: 33)
Exomes 𝑓: 0.0035 ( 231 hom. )
Consequence
ZBTB17
NM_003443.3 intron
NM_003443.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
ZBTB17 (HGNC:12936): (zinc finger and BTB domain containing 17) This gene encodes a zinc finger protein involved in the regulation of c-myc. The symbol MIZ1 has also been associated with PIAS2 which is a different gene located on chromosome 18. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 1-15944172-CTGGGTGAACAAGCTGA-C is Benign according to our data. Variant chr1-15944172-CTGGGTGAACAAGCTGA-C is described in ClinVar as [Benign]. Clinvar id is 1262168.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB17 | NM_003443.3 | c.1371+112_1371+127del | intron_variant | ENST00000375743.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB17 | ENST00000375743.9 | c.1371+112_1371+127del | intron_variant | 1 | NM_003443.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0340 AC: 5179AN: 152170Hom.: 282 Cov.: 33
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GnomAD3 exomes AF: 0.00716 AC: 974AN: 136122Hom.: 50 AF XY: 0.00569 AC XY: 418AN XY: 73458
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GnomAD4 exome AF: 0.00351 AC: 4298AN: 1223560Hom.: 231 AF XY: 0.00299 AC XY: 1826AN XY: 611154
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GnomAD4 genome AF: 0.0340 AC: 5184AN: 152288Hom.: 282 Cov.: 33 AF XY: 0.0334 AC XY: 2491AN XY: 74472
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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
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 26, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at