Genetic Variant ENST00000512327.1:n.287A>G (chr3-141386728-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000512327.1(ZBTB38):n.287A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,470 control chromosomes in the GnomAD database, including 21,902 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 0.51 ( 21862 hom., cov: 32)

Exomes 𝑓: 0.44 ( 40 hom. )

Consequence

ZBTB38
ENST00000512327.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.138

Publications

122 publications found

Variant links:

COSMIC-nc: COSV72286607

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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512327.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZBTB38	NM_001376113.1	MANE Select	c.-171-144A>G	intron	N/A	NP_001363042.1
ZBTB38	NM_001350099.2		c.-389A>G	5_prime_UTR	Exon 1 of 6	NP_001337028.1
ZBTB38	NM_001376157.1		c.-199A>G	5_prime_UTR	Exon 1 of 4	NP_001363086.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZBTB38	ENST00000512327.1	TSL:1	n.287A>G	non_coding_transcript_exon	Exon 1 of 2
ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.-171-144A>G	intron	N/A	ENSP00000372635.5
ZBTB38	ENST00000509842.5	TSL:1	c.-416-144A>G	intron	N/A	ENSP00000426931.1

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

77973

AN:

151914

Hom.:

21824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.754

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.441

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.438

Gnomad OTH

AF:

0.437

GnomAD4 exome

AF:

0.438

AC:

191

AN:

436

Hom.:

Cov.:

AF XY:

0.427

AC XY:

112

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.437

AC:

186

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.514

AC:

78074

AN:

152034

Hom.:

21862

Cov.:

AF XY:

0.507

AC XY:

37660

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.754

AC:

31265

AN:

41460

American (AMR)

AF:

0.435

AC:

6643

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.397

AC:

1380

AN:

3472

East Asian (EAS)

AF:

0.324

AC:

1678

AN:

5172

South Asian (SAS)

AF:

0.291

AC:

1399

AN:

4810

European-Finnish (FIN)

AF:

0.441

AC:

4667

AN:

10578

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.438

AC:

29734

AN:

67954

Other (OTH)

AF:

0.437

AC:

922

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1794

3588

5381

7175

8969

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<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:

0.448

Hom.:

69744

Bravo

AF:

0.521

Asia WGS

AF:

0.307

AC:

1066

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.0

(source)

DANN

Benign

0.78

PhyloP100

-0.14

PromoterAI

0.038

Neutral

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over