Genetic Variant ZBTB38:c.-232T>C (chr3-141396377-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080412.3(ZBTB38):c.-232T>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 0.526 in 154,892 control chromosomes in the GnomAD database, including 24,177 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 ( 23927 hom., cov: 32)

Exomes 𝑓: 0.41 ( 250 hom. )

Consequence

ZBTB38
NM_001080412.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Publications

29 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]

ZBTB38 links:

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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=-1.07).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080412.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZBTB38	NM_001376113.1	MANE Select	c.-105-7550T>C	intron	N/A	NP_001363042.1	Q8NAP3
ZBTB38	NM_001080412.3		c.-232T>C	5_prime_UTR	Exon 6 of 8	NP_001073881.2	Q8NAP3
ZBTB38	NM_001376114.1		c.-232T>C	5_prime_UTR	Exon 5 of 7	NP_001363043.1	Q8NAP3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZBTB38	ENST00000509842.5	TSL:1	c.-232T>C	5_prime_UTR	Exon 6 of 8	ENSP00000426931.1	D6RE69
ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.-105-7550T>C	intron	N/A	ENSP00000372635.5	Q8NAP3
ZBTB38	ENST00000509883.5	TSL:1	c.-105-7550T>C	intron	N/A	ENSP00000424254.1	D6RBC4

Frequencies

GnomAD3 genomes

AF:

0.527

AC:

80166

AN:

151994

Hom.:

23877

Cov.:

show subpopulations

Gnomad AFR

AF:

0.821

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.437

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.449

GnomAD4 exome

AF:

0.405

AC:

1127

AN:

2780

Hom.:

250

Cov.:

AF XY:

0.388

AC XY:

720

AN XY:

1858

show subpopulations

African (AFR)

AF:

0.724

AC:

AN:

American (AMR)

AF:

0.443

AC:

AN:

140

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

AN:

East Asian (EAS)

AF:

0.170

AC:

AN:

194

South Asian (SAS)

AF:

0.284

AC:

AN:

148

European-Finnish (FIN)

AF:

0.466

AC:

AN:

Middle Eastern (MID)

AF:

0.444

AC:

AN:

European-Non Finnish (NFE)

AF:

0.420

AC:

827

AN:

1968

Other (OTH)

AF:

0.444

AC:

AN:

126

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

116

145

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.528

AC:

80282

AN:

152112

Hom.:

23927

Cov.:

AF XY:

0.519

AC XY:

38609

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.822

AC:

34114

AN:

41526

American (AMR)

AF:

0.428

AC:

6549

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1380

AN:

3470

East Asian (EAS)

AF:

0.221

AC:

1145

AN:

5186

South Asian (SAS)

AF:

0.304

AC:

1465

AN:

4820

European-Finnish (FIN)

AF:

0.437

AC:

4606

AN:

10546

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.437

AC:

29688

AN:

67950

Other (OTH)

AF:

0.449

AC:

950

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1704

3408

5111

6815

8519

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.476

Hom.:

2239

Bravo

AF:

0.537

Asia WGS

AF:

0.290

AC:

1010

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.15

(source)

DANN

Benign

0.31

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over