dbSNP rs11665417: ZBTB14:c.-82+28G>A (chr18-5293944-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001243702.2(ZBTB14):c.-82+28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,822 control chromosomes in the GnomAD database, including 13,324 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 0.41 ( 13324 hom., cov: 33)

Exomes 𝑓: 0.42 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

ZBTB14
NM_001243702.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

7 publications found

Variant links:

Genes affected

ZBTB14 (HGNC:12860): (zinc finger and BTB domain containing 14) Enables DNA-binding transcription factor activity and transcription cis-regulatory region binding activity. Involved in negative regulation of transcription, DNA-templated. Located in aggresome; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB14 links:

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 = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001243702.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZBTB14	NM_001243702.2	MANE Select	c.-82+28G>A	intron	N/A	NP_001230631.1	O43829
ZBTB14	NM_001143823.3		c.-82+28G>A	intron	N/A	NP_001137295.1	O43829
ZBTB14	NM_001243704.2		c.-82+28G>A	intron	N/A	NP_001230633.1	O43829

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZBTB14	ENST00000651870.1	MANE Select	c.-82+28G>A	intron	N/A	ENSP00000499212.1	O43829
ZBTB14	ENST00000357006.8	TSL:1	c.-82+28G>A	intron	N/A	ENSP00000349503.4	O43829
ZBTB14	ENST00000400143.7	TSL:1	c.-81-617G>A	intron	N/A	ENSP00000383009.3	O43829

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62368

AN:

151702

Hom.:

13313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.467

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.0736

Gnomad SAS

AF:

0.437

Gnomad FIN

AF:

0.387

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.386

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.417

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.411

AC:

62407

AN:

151822

Hom.:

13324

Cov.:

AF XY:

0.407

AC XY:

30217

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.467

AC:

19318

AN:

41350

American (AMR)

AF:

0.336

AC:

5126

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1677

AN:

3466

East Asian (EAS)

AF:

0.0736

AC:

381

AN:

5180

South Asian (SAS)

AF:

0.436

AC:

2102

AN:

4822

European-Finnish (FIN)

AF:

0.387

AC:

4066

AN:

10514

Middle Eastern (MID)

AF:

0.446

AC:

131

AN:

294

European-Non Finnish (NFE)

AF:

0.419

AC:

28456

AN:

67904

Other (OTH)

AF:

0.389

AC:

820

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1881

3763

5644

7526

9407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.414

Hom.:

2808

Bravo

AF:

0.407

Asia WGS

AF:

0.302

AC:

1050

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.55

(source)

DANN

Benign

0.76

PhyloP100

-1.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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