rs9821337

Variant summary

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

The NM_001376113.1(ZBTB38):​c.-234-4082C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,176 control chromosomes in the GnomAD database, including 7,959 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 0.31 ( 7959 hom., cov: 33)

Consequence

ZBTB38
NM_001376113.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.300
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZBTB38NM_001376113.1 linkuse as main transcriptc.-234-4082C>G intron_variant ENST00000321464.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZBTB38ENST00000321464.7 linkuse as main transcriptc.-234-4082C>G intron_variant NM_001376113.1 P1

Frequencies

GnomAD3 genomes
AF:
0.311
AC:
47288
AN:
152058
Hom.:
7947
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.353
Gnomad AMI
AF:
0.273
Gnomad AMR
AF:
0.198
Gnomad ASJ
AF:
0.315
Gnomad EAS
AF:
0.00308
Gnomad SAS
AF:
0.170
Gnomad FIN
AF:
0.364
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.338
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.311
AC:
47330
AN:
152176
Hom.:
7959
Cov.:
33
AF XY:
0.303
AC XY:
22580
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.353
Gnomad4 AMR
AF:
0.197
Gnomad4 ASJ
AF:
0.315
Gnomad4 EAS
AF:
0.00308
Gnomad4 SAS
AF:
0.171
Gnomad4 FIN
AF:
0.364
Gnomad4 NFE
AF:
0.338
Gnomad4 OTH
AF:
0.266
Alfa
AF:
0.329
Hom.:
1060
Bravo
AF:
0.300
Asia WGS
AF:
0.0990
AC:
347
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.1
DANN
Benign
0.35

Splicing

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: rs9821337; hg19: chr3-141096185; API