dbSNP rs990072: ZBTB14:c.*659A>G (chr18-5290199-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_001243702.2(ZBTB14):c.*659A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,958 control chromosomes in the GnomAD database, including 26,779 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 0.59 ( 26771 hom., cov: 32)

Exomes 𝑓: 0.57 ( 8 hom. )

Consequence

ZBTB14
NM_001243702.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.566

Publications

15 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:

LINC00667 (HGNC:27906): (long intergenic non-protein coding RNA 667)

LINC00667 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 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.*659A>G	3_prime_UTR	Exon 4 of 4	NP_001230631.1	O43829
ZBTB14	NM_001143823.3		c.*659A>G	3_prime_UTR	Exon 4 of 4	NP_001137295.1	O43829
ZBTB14	NM_001243704.2		c.*659A>G	3_prime_UTR	Exon 4 of 4	NP_001230633.1	O43829

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZBTB14	ENST00000651870.1	MANE Select	c.*659A>G	3_prime_UTR	Exon 4 of 4	ENSP00000499212.1	O43829
ZBTB14	ENST00000357006.8	TSL:1	c.*659A>G	3_prime_UTR	Exon 4 of 4	ENSP00000349503.4	O43829
ZBTB14	ENST00000614697.4	TSL:2	c.*659A>G	3_prime_UTR	Exon 4 of 4	ENSP00000484129.1	O43829

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89444

AN:

151800

Hom.:

26724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.484

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.588

Gnomad EAS

AF:

0.787

Gnomad SAS

AF:

0.665

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.539

Gnomad OTH

AF:

0.557

GnomAD4 exome

AF:

0.571

AC:

AN:

Hom.:

Cov.:

AF XY:

0.583

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.528

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.589

AC:

89547

AN:

151916

Hom.:

26771

Cov.:

AF XY:

0.592

AC XY:

43976

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.647

AC:

26782

AN:

41406

American (AMR)

AF:

0.613

AC:

9364

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.588

AC:

2038

AN:

3466

East Asian (EAS)

AF:

0.788

AC:

4068

AN:

5162

South Asian (SAS)

AF:

0.664

AC:

3202

AN:

4824

European-Finnish (FIN)

AF:

0.540

AC:

5683

AN:

10526

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.539

AC:

36592

AN:

67934

Other (OTH)

AF:

0.562

AC:

1186

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1849

3698

5547

7396

9245

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<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:

0.552

Hom.:

30063

Bravo

AF:

0.592

Asia WGS

AF:

0.720

AC:

2504

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

(source)

DANN

Benign

0.47

PhyloP100

-0.57

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