3-141414608-G-A

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.920

Publications

51 publications found
Variant links:
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]

Genome browser will be placed here

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
ZBTB38NM_001376113.1 linkc.-1+10577G>A intron_variant Intron 5 of 5 ENST00000321464.7 NP_001363042.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZBTB38ENST00000321464.7 linkc.-1+10577G>A intron_variant Intron 5 of 5 6 NM_001376113.1 ENSP00000372635.5 Q8NAP3

Frequencies

GnomAD3 genomes
AF:
0.488
AC:
74066
AN:
151842
Hom.:
19490
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.690
Gnomad AMI
AF:
0.340
Gnomad AMR
AF:
0.410
Gnomad ASJ
AF:
0.387
Gnomad EAS
AF:
0.222
Gnomad SAS
AF:
0.288
Gnomad FIN
AF:
0.438
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.434
Gnomad OTH
AF:
0.424
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.488
AC:
74167
AN:
151960
Hom.:
19528
Cov.:
31
AF XY:
0.480
AC XY:
35670
AN XY:
74252
show subpopulations
African (AFR)
AF:
0.691
AC:
28625
AN:
41452
American (AMR)
AF:
0.410
AC:
6266
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.387
AC:
1342
AN:
3464
East Asian (EAS)
AF:
0.222
AC:
1145
AN:
5162
South Asian (SAS)
AF:
0.287
AC:
1378
AN:
4806
European-Finnish (FIN)
AF:
0.438
AC:
4628
AN:
10558
Middle Eastern (MID)
AF:
0.337
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
0.434
AC:
29477
AN:
67916
Other (OTH)
AF:
0.424
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:
0.453
Hom.:
32917
Bravo
AF:
0.492
Asia WGS
AF:
0.273
AC:
948
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.25
DANN
Benign
0.69
PhyloP100
-0.92
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1991431; hg19: chr3-141133450; API