Genetic Variant NM_001207005.2:c.1983delG (chr19-44274642-CG-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001207005.2(ZNF233):c.1983delG(p.Leu662CysfsTer44) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,605,746 control chromosomes in the GnomAD database, including 29,711 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 8690 hom., cov: 25)

Exomes 𝑓: 0.15 ( 21021 hom. )

Consequence

ZNF233
NM_001207005.2 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.53

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 19-44274642-CG-C is Benign according to our data. Variant chr19-44274642-CG-C is described in ClinVar as [Benign]. Clinvar id is 403624.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF233	NM_001207005.2 link	c.1983delG	p.Leu662CysfsTer44	frameshift_variant	Exon 5 of 5	ENST00000683810.1	NP_001193934.1	A6NK53

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF233	ENST00000683810.1 link	c.1983delG	p.Leu662CysfsTer44	frameshift_variant	Exon 5 of 5		NM_001207005.2	ENSP00000507588.1		A6NK53

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41477

AN:

151608

Hom.:

8651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.584

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.233

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.210

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.248

GnomAD3 exomes

AF:

0.198

AC:

48948

AN:

247128

Hom.:

6802

AF XY:

0.181

AC XY:

24205

AN XY:

133560

show subpopulations

Gnomad AFR exome

AF:

0.588

Gnomad AMR exome

AF:

0.343

Gnomad ASJ exome

AF:

0.215

Gnomad EAS exome

AF:

0.234

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.137

Gnomad NFE exome

AF:

0.126

Gnomad OTH exome

AF:

0.182

GnomAD4 exome

AF:

0.147

AC:

213986

AN:

1454020

Hom.:

21021

Cov.:

AF XY:

0.145

AC XY:

104729

AN XY:

722466

show subpopulations

Gnomad4 AFR exome

AF:

0.606

Gnomad4 AMR exome

AF:

0.335

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.222

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.122

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.274

AC:

41582

AN:

151726

Hom.:

8690

Cov.:

AF XY:

0.274

AC XY:

20334

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.584

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.209

Gnomad4 EAS

AF:

0.233

Gnomad4 SAS

AF:

0.111

Gnomad4 FIN

AF:

0.142

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.0992

Hom.:

227

Bravo

AF:

0.306

Asia WGS

AF:

0.217

AC:

755

AN:

3478

EpiCase

AF:

0.129

EpiControl

AF:

0.137

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes:652/2178=29.93% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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