rs2232447
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014797.3(ZBTB24):āc.1389C>Gā(p.Ser463=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00333 in 1,612,386 control chromosomes in the GnomAD database, including 173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.018 ( 93 hom., cov: 32)
Exomes š: 0.0018 ( 80 hom. )
Consequence
ZBTB24
NM_014797.3 synonymous
NM_014797.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0160
Genes affected
ZBTB24 (HGNC:21143): (zinc finger and BTB domain containing 24) Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in nucleus. Implicated in immunodeficiency-centromeric instability-facial anomalies syndrome 2. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 6-109466556-G-C is Benign according to our data. Variant chr6-109466556-G-C is described in ClinVar as [Benign]. Clinvar id is 472198.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0611 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZBTB24 | NM_014797.3 | c.1389C>G | p.Ser463= | synonymous_variant | 7/7 | ENST00000230122.4 | NP_055612.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZBTB24 | ENST00000230122.4 | c.1389C>G | p.Ser463= | synonymous_variant | 7/7 | 1 | NM_014797.3 | ENSP00000230122 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0180 AC: 2736AN: 152134Hom.: 93 Cov.: 32
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GnomAD3 exomes AF: 0.00434 AC: 1080AN: 248688Hom.: 33 AF XY: 0.00330 AC XY: 446AN XY: 135070
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GnomAD4 exome AF: 0.00180 AC: 2621AN: 1460134Hom.: 80 Cov.: 33 AF XY: 0.00150 AC XY: 1088AN XY: 726470
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GnomAD4 genome AF: 0.0180 AC: 2742AN: 152252Hom.: 93 Cov.: 32 AF XY: 0.0174 AC XY: 1299AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Immunodeficiency-centromeric instability-facial anomalies syndrome 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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