Genetic Variant ZNF532:c.2528+856T>C (chr18-58935470-T-C) – 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.2528+856T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.17 ( 468 hom., cov: 5)

Consequence

ZNF532
NM_001375912.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

2 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF532	NM_001375912.1 link	c.2528+856T>C		intron_variant	Intron 4 of 9	ENST00000591808.6	NP_001362841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF532	ENST00000591808.6 link	c.2528+856T>C		intron_variant	Intron 4 of 9	1	NM_001375912.1	ENSP00000468238.1		Q9HCE3

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

2838

AN:

16648

Hom.:

463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.119

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.0535

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.286

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.152

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.171

AC:

2848

AN:

16682

Hom.:

468

Cov.:

AF XY:

0.179

AC XY:

1462

AN XY:

8174

show subpopulations

African (AFR)

AF:

0.264

AC:

785

AN:

2968

American (AMR)

AF:

0.117

AC:

183

AN:

1570

Ashkenazi Jewish (ASJ)

AF:

0.293

AC:

103

AN:

352

East Asian (EAS)

AF:

0.0544

AC:

AN:

956

South Asian (SAS)

AF:

0.230

AC:

100

AN:

434

European-Finnish (FIN)

AF:

0.191

AC:

187

AN:

980

Middle Eastern (MID)

AF:

0.286

AC:

AN:

European-Non Finnish (NFE)

AF:

0.152

AC:

1373

AN:

9008

Other (OTH)

AF:

0.160

AC:

AN:

212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

178

267

356

445

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

150

<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:

0.387

Hom.:

1075

Bravo

AF:

0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.3

(source)

DANN

Benign

0.36

PhyloP100

-1.4

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over