Variant 19-44267008-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001207005.2(ZNF233):c.238+47T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00503 in 1,447,646 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0039 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0052 ( 22 hom. )

Consequence

ZNF233
NM_001207005.2 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.880

Variant links:

Genes affected

ZNF233 (HGNC:30946): (zinc finger protein 233) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF233 links:

ZNF235 (HGNC:12866): (zinc finger protein 235) This gene product belongs to the zinc finger protein superfamily, members of which are regulatory proteins characterized by nucleic acid-binding zinc finger domains. The encoded protein is a member of the Kruppel family of zinc finger proteins, and contains Kruppel-associated box (KRAB) A and B domains and 15 tandemly arrayed C2H2-type zinc fingers. It is an ortholog of the mouse Zfp93 protein. This gene is located in a cluster of zinc finger genes on 19q13.2. [provided by RefSeq, Jul 2008]

ZNF235 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 19-44267008-T-A is Benign according to our data. Variant chr19-44267008-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650077.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF233	NM_001207005.2 linkuse as main transcript	c.238+47T>A		intron_variant		ENST00000683810.1	NP_001193934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF233	ENST00000683810.1 linkuse as main transcript	c.238+47T>A		intron_variant			NM_001207005.2	ENSP00000507588	P1

Frequencies

GnomAD3 genomes

AF:

0.00394

AC:

600

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00373

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00896

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00563

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00398

AC:

843

AN:

211952

Hom.:

AF XY:

0.00397

AC XY:

458

AN XY:

115362

show subpopulations

Gnomad AFR exome

AF:

0.000668

Gnomad AMR exome

AF:

0.00223

Gnomad ASJ exome

AF:

0.000560

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000931

Gnomad FIN exome

AF:

0.0108

Gnomad NFE exome

AF:

0.00522

Gnomad OTH exome

AF:

0.00462

GnomAD4 exome

AF:

0.00516

AC:

6686

AN:

1295392

Hom.:

Cov.:

AF XY:

0.00509

AC XY:

3298

AN XY:

648278

show subpopulations

Gnomad4 AFR exome

AF:

0.000674

Gnomad4 AMR exome

AF:

0.00231

Gnomad4 ASJ exome

AF:

0.000833

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000833

Gnomad4 FIN exome

AF:

0.0106

Gnomad4 NFE exome

AF:

0.00581

Gnomad4 OTH exome

AF:

0.00462

GnomAD4 genome

AF:

0.00394

AC:

600

AN:

152254

Hom.:

Cov.:

AF XY:

0.00419

AC XY:

312

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00123

Gnomad4 AMR

AF:

0.00373

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00896

Gnomad4 NFE

AF:

0.00563

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00538

Hom.:

Bravo

AF:

0.00281

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

ZNF233: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.90

DANN

Benign

0.82

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over