Genetic Variant ZNF532:c.-18+9C>T (chr18-58865588-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001375912.1(ZNF532):c.-18+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,882 control chromosomes in the GnomAD database, including 6,016 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 0.28 ( 5973 hom., cov: 32)

Exomes 𝑓: 0.27 ( 43 hom. )

Consequence

ZNF532
NM_001375912.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.702

Publications

7 publications found

Variant links:

Genes affected

ZNF532 (HGNC:30940): (zinc finger protein 532) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF532 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375912.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF532	NM_001375912.1	MANE Select	c.-18+9C>T	intron	N/A	NP_001362841.1
ZNF532	NM_001318726.2		c.-18+9C>T	intron	N/A	NP_001305655.1
ZNF532	NM_001318727.2		c.-18+9C>T	intron	N/A	NP_001305656.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF532	ENST00000591808.6	TSL:1 MANE Select	c.-18+9C>T	intron	N/A	ENSP00000468238.1
ZNF532	ENST00000336078.8	TSL:1	c.-18+9C>T	intron	N/A	ENSP00000338217.4
ZNF532	ENST00000591083.5	TSL:1	c.-18+9C>T	intron	N/A	ENSP00000468532.1

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41830

AN:

151854

Hom.:

5970

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.283

GnomAD4 exome

AF:

0.274

AC:

249

AN:

910

Hom.:

Cov.:

AF XY:

0.258

AC XY:

122

AN XY:

472

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.284

AC:

187

AN:

658

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.268

AC:

AN:

112

Other (OTH)

AF:

0.239

AC:

AN:

134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.275

AC:

41853

AN:

151972

Hom.:

5973

Cov.:

AF XY:

0.275

AC XY:

20450

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.349

AC:

14453

AN:

41422

American (AMR)

AF:

0.202

AC:

3078

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.388

AC:

1347

AN:

3468

East Asian (EAS)

AF:

0.190

AC:

982

AN:

5174

South Asian (SAS)

AF:

0.264

AC:

1272

AN:

4814

European-Finnish (FIN)

AF:

0.272

AC:

2864

AN:

10544

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.249

AC:

16944

AN:

67974

Other (OTH)

AF:

0.282

AC:

593

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1564

3128

4692

6256

7820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.260

Hom.:

17196

Bravo

AF:

0.276

Asia WGS

AF:

0.238

AC:

828

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.4

(source)

DANN

Benign

0.81

PhyloP100

-0.70

PromoterAI

-0.012

Neutral

(source)

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