Variant 19-35715395-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014383.3(ZBTB32):c.769G>A(p.Gly257Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,459,452 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

ZBTB32
NM_014383.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.33

Variant links:

Genes affected

ZBTB32 (HGNC:16763): (zinc finger and BTB domain containing 32) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; identical protein binding activity; and sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB32 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.1579817).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB32	NM_014383.3 linkuse as main transcript	c.769G>A	p.Gly257Arg	missense_variant	3/7	ENST00000392197.7	NP_055198.1	Q9Y2Y4
ZBTB32	NM_001316902.2 linkuse as main transcript	c.6-68G>A		intron_variant			NP_001303831.1	Q9Y2Y4
ZBTB32	NM_001316903.2 linkuse as main transcript	c.-86-68G>A		intron_variant			NP_001303832.1	Q9Y2Y4
ZBTB32	XM_017026591.2 linkuse as main transcript	c.6-68G>A		intron_variant			XP_016882080.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZBTB32	ENST00000392197.7 linkuse as main transcript	c.769G>A	p.Gly257Arg	missense_variant	3/7	5	NM_014383.3	ENSP00000376035.1	Q9Y2Y4
ZBTB32	ENST00000262630.7 linkuse as main transcript	c.769G>A	p.Gly257Arg	missense_variant	2/6	1		ENSP00000262630.3	Q9Y2Y4
ZBTB32	ENST00000481182.1 linkuse as main transcript	n.769G>A		non_coding_transcript_exon_variant	2/4	1		ENSP00000433657.1	A0A0C4DGF1
ZBTB32	ENST00000426659.6 linkuse as main transcript	c.-86-68G>A		intron_variant		3		ENSP00000466524.1	K7EMJ1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000812

AC:

AN:

246266

Hom.:

AF XY:

0.00000747

AC XY:

AN XY:

133880

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000206

AC:

AN:

1459452

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726150

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 12, 2024

The c.769G>A (p.G257R) alteration is located in exon 2 (coding exon 1) of the ZBTB32 gene. This alteration results from a G to A substitution at nucleotide position 769, causing the glycine (G) at amino acid position 257 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.37

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.10

T;T

Eigen

Benign

-0.19

Eigen_PC

Benign

0.023

FATHMM_MKL

Benign

0.46

LIST_S2

Benign

0.77

.;T

M_CAP

Benign

0.0087

MetaRNN

Benign

0.16

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

N;N

MutationTaster

Benign

0.65

N;N

PrimateAI

Benign

0.34

PROVEAN

Benign

-0.16

N;N

REVEL

Benign

0.049

Sift

Benign

0.040

D;D

Sift4G

Benign

0.21

T;T

Polyphen

0.15

B;B

Vest4

0.20

MutPred

0.57

Gain of MoRF binding (P = 0.0188);Gain of MoRF binding (P = 0.0188);

MVP

0.64

MPC

0.50

ClinPred

0.49

GERP RS

5.3

Varity_R

0.12

gMVP

0.083

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over