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GeneBe

rs6440006

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001376113.1(ZBTB38):c.1-18540G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,042 control chromosomes in the GnomAD database, including 24,632 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 0.54 ( 24632 hom., cov: 33)

Consequence

ZBTB38
NM_001376113.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33
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]

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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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZBTB38NM_001376113.1 linkuse as main transcriptc.1-18540G>A intron_variant ENST00000321464.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZBTB38ENST00000321464.7 linkuse as main transcriptc.1-18540G>A intron_variant NM_001376113.1 P1

Frequencies

GnomAD3 genomes
AF:
0.538
AC:
81745
AN:
151924
Hom.:
24585
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.829
Gnomad AMI
AF:
0.321
Gnomad AMR
AF:
0.454
Gnomad ASJ
AF:
0.426
Gnomad EAS
AF:
0.331
Gnomad SAS
AF:
0.298
Gnomad FIN
AF:
0.441
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.439
Gnomad OTH
AF:
0.466
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.538
AC:
81855
AN:
152042
Hom.:
24632
Cov.:
33
AF XY:
0.531
AC XY:
39474
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.829
Gnomad4 AMR
AF:
0.454
Gnomad4 ASJ
AF:
0.426
Gnomad4 EAS
AF:
0.331
Gnomad4 SAS
AF:
0.297
Gnomad4 FIN
AF:
0.441
Gnomad4 NFE
AF:
0.439
Gnomad4 OTH
AF:
0.466
Alfa
AF:
0.470
Hom.:
4118
Bravo
AF:
0.551
Asia WGS
AF:
0.308
AC:
1070
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
0.090
Dann
Benign
0.60

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6440006; hg19: chr3-141142691; API