rs11660954

chr18-58936571-G-A

Variant summary

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

The NM_001375912.1(ZNF532):c.2528+1957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,104 control chromosomes in the GnomAD database, including 4,782 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 0.22 (4782 hom., cov: 32)
• Consequence: ZNF532 NM_001375912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF532	NM_001375912.1	c.2528+1957G>A		intron_variant		ENST00000591808.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF532	ENST00000591808.6	c.2528+1957G>A		intron_variant		1	NM_001375912.1	P1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33645 AN: 151986 Hom.: 4780 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.221 AC: 33652 AN: 152104 Hom.: 4782 Cov.: 32 AF XY: 0.222 AC XY: 16475 AN XY: 74330

Gnomad4 AFR AF: 0.0718

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.241

Alfa AF: 0.264 Hom.: 747

Bravo AF: 0.203

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.84
Dann	Benign	0.67

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: rs11660954; hg19: chr18-56603803;