rs2871960
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000513570.1(ZBTB38):c.-286A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,210 control chromosomes in the GnomAD database, including 24,289 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.53 ( 24279 hom., cov: 32)
Exomes 𝑓: 0.41 ( 10 hom. )
Consequence
ZBTB38
ENST00000513570.1 5_prime_UTR
ENST00000513570.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.293
Genes affected
ZBTB38 (HGNC:26636): (zinc finger and BTB domain containing 38) The protein encoded by this gene is a zinc finger transcriptional activator that binds methylated DNA. The encoded protein can form homodimers or heterodimers through the zinc finger domains. In mouse, inhibition of this protein has been associated with apoptosis in some cell types. [provided by RefSeq, Jun 2010]
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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=-0.65).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB38 | NM_001376113.1 | c.-105-955A>C | intron_variant | ENST00000321464.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB38 | ENST00000321464.7 | c.-105-955A>C | intron_variant | NM_001376113.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.534 AC: 81141AN: 151996Hom.: 24231 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.406 AC: 39AN: 96Hom.: 10 Cov.: 0 AF XY: 0.417 AC XY: 35AN XY: 84
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GnomAD4 genome ? AF: 0.534 AC: 81254AN: 152114Hom.: 24279 Cov.: 32 AF XY: 0.527 AC XY: 39169AN XY: 74360
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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