Variant rs11665417 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB14	NM_001243702.2 linkuse as main transcript	c.-82+28G>A		intron_variant		ENST00000651870.1	NP_001230631.1	O43829

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB14	ENST00000651870.1 linkuse as main transcript	c.-82+28G>A		intron_variant			NM_001243702.2	ENSP00000499212.1		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

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.411

AC:

62407

AN:

151822

Hom.:

13324

Cov.:

AF XY:

0.407

AC XY:

30217

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.467

Gnomad4 AMR

AF:

0.336

Gnomad4 ASJ

AF:

0.484

Gnomad4 EAS

AF:

0.0736

Gnomad4 SAS

AF:

0.436

Gnomad4 FIN

AF:

0.387

Gnomad4 NFE

AF:

0.419

Gnomad4 OTH

AF:

0.389

Alfa

AF:

0.413

Hom.:

2718

Bravo

AF:

0.407

Asia WGS

AF:

0.302

AC:

1050

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.55

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over