3-141414608-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001376113.1(ZBTB38):c.-1+10577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,960 control chromosomes in the GnomAD database, including 19,528 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 0.49 ( 19528 hom., cov: 31)
Consequence
ZBTB38
NM_001376113.1 intron
NM_001376113.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.920
Publications
51 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZBTB38 | NM_001376113.1 | c.-1+10577G>A | intron_variant | Intron 5 of 5 | ENST00000321464.7 | NP_001363042.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.488 AC: 74066AN: 151842Hom.: 19490 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
74066
AN:
151842
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.488 AC: 74167AN: 151960Hom.: 19528 Cov.: 31 AF XY: 0.480 AC XY: 35670AN XY: 74252 show subpopulations
GnomAD4 genome
AF:
AC:
74167
AN:
151960
Hom.:
Cov.:
31
AF XY:
AC XY:
35670
AN XY:
74252
show subpopulations
African (AFR)
AF:
AC:
28625
AN:
41452
American (AMR)
AF:
AC:
6266
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
1342
AN:
3464
East Asian (EAS)
AF:
AC:
1145
AN:
5162
South Asian (SAS)
AF:
AC:
1378
AN:
4806
European-Finnish (FIN)
AF:
AC:
4628
AN:
10558
Middle Eastern (MID)
AF:
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
AC:
29477
AN:
67916
Other (OTH)
AF:
AC:
897
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1790
3580
5371
7161
8951
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
640
1280
1920
2560
3200
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
948
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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