chr1-15941940-TTAAA-T
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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.*25_*28del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00295 in 1,574,684 control chromosomes in the GnomAD database, including 207 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0060 ( 39 hom., cov: 33)
Exomes 𝑓: 0.0026 ( 168 hom. )
Consequence
ZBTB17
NM_003443.3 3_prime_UTR
NM_003443.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.47
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 1-15941940-TTAAA-T is Benign according to our data. Variant chr1-15941940-TTAAA-T is described in ClinVar as [Benign]. Clinvar id is 1238751.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0764 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB17 | NM_003443.3 | c.*25_*28del | 3_prime_UTR_variant | 16/16 | ENST00000375743.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB17 | ENST00000375743.9 | c.*25_*28del | 3_prime_UTR_variant | 16/16 | 1 | NM_003443.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00599 AC: 912AN: 152174Hom.: 39 Cov.: 33
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GnomAD3 exomes AF: 0.0131 AC: 2894AN: 220750Hom.: 143 AF XY: 0.00961 AC XY: 1166AN XY: 121290
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GnomAD4 exome AF: 0.00262 AC: 3727AN: 1422392Hom.: 168 AF XY: 0.00221 AC XY: 1554AN XY: 704086
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GnomAD4 genome AF: 0.00601 AC: 916AN: 152292Hom.: 39 Cov.: 33 AF XY: 0.00709 AC XY: 528AN XY: 74470
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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 21, 2021 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at