chr18-58935470-T-C

Position:

• chr18-58935470-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF532	NM_001375912.1	c.2528+856T>C		intron_variant		ENST00000591808.6	NP_001362841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF532	ENST00000591808.6	c.2528+856T>C		intron_variant		1	NM_001375912.1	ENSP00000468238.1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 2838 AN: 16648 Hom.: 463 Cov.: 5

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.: 5 AF XY: 0.179 AC XY: 1462 AN XY: 8174

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0544

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.160

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
DANN	Benign	0.36

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

Other links and lift over

dbSNP: rs73439953; hg19: chr18-56602702;