rs848217
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_003443.3(ZBTB17):āc.621T>Cā(p.Ala207=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 1,605,680 control chromosomes in the GnomAD database, including 207,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.50 ( 19516 hom., cov: 32)
Exomes š: 0.51 ( 187960 hom. )
Consequence
ZBTB17
NM_003443.3 synonymous
NM_003443.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.811
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 1-15945755-A-G is Benign according to our data. Variant chr1-15945755-A-G is described in ClinVar as [Benign]. Clinvar id is 1264129.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.811 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB17 | NM_003443.3 | c.621T>C | p.Ala207= | synonymous_variant | 6/16 | ENST00000375743.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB17 | ENST00000375743.9 | c.621T>C | p.Ala207= | synonymous_variant | 6/16 | 1 | NM_003443.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.503 AC: 76316AN: 151820Hom.: 19480 Cov.: 32
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GnomAD3 exomes AF: 0.530 AC: 128442AN: 242426Hom.: 35251 AF XY: 0.528 AC XY: 69776AN XY: 132188
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GnomAD4 exome AF: 0.506 AC: 735040AN: 1453742Hom.: 187960 Cov.: 70 AF XY: 0.508 AC XY: 367455AN XY: 723584
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GnomAD4 genome ? AF: 0.503 AC: 76406AN: 151938Hom.: 19516 Cov.: 32 AF XY: 0.509 AC XY: 37784AN XY: 74276
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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 05, 2021 | - - |
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