rs9661939
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_003443.3(ZBTB17):c.1002C>T(p.Phe334=) variant causes a synonymous change. The variant allele was found at a frequency of 0.287 in 1,612,314 control chromosomes in the GnomAD database, including 71,173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.24 ( 5174 hom., cov: 33)
Exomes 𝑓: 0.29 ( 65999 hom. )
Consequence
ZBTB17
NM_003443.3 synonymous
NM_003443.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.87
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 1-15944765-G-A is Benign according to our data. Variant chr1-15944765-G-A is described in ClinVar as [Benign]. Clinvar id is 1280656.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB17 | NM_003443.3 | c.1002C>T | p.Phe334= | synonymous_variant | 8/16 | ENST00000375743.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB17 | ENST00000375743.9 | c.1002C>T | p.Phe334= | synonymous_variant | 8/16 | 1 | NM_003443.3 | P2 | |
ZBTB17 | ENST00000375733.6 | c.1002C>T | p.Phe334= | synonymous_variant | 8/16 | 1 | A2 | ||
ZBTB17 | ENST00000537142.5 | c.756C>T | p.Phe252= | synonymous_variant | 7/15 | 2 | |||
ZBTB17 | ENST00000492834.1 | n.711C>T | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.238 AC: 36276AN: 152108Hom.: 5166 Cov.: 33
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GnomAD3 exomes AF: 0.285 AC: 69731AN: 244386Hom.: 11285 AF XY: 0.297 AC XY: 39320AN XY: 132540
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GnomAD4 exome AF: 0.292 AC: 426841AN: 1460088Hom.: 65999 Cov.: 76 AF XY: 0.298 AC XY: 216202AN XY: 726294
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GnomAD4 genome ? AF: 0.239 AC: 36310AN: 152226Hom.: 5174 Cov.: 33 AF XY: 0.240 AC XY: 17893AN XY: 74420
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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