chr18-58936571-G-A

Variant names:

• chr18-58936571-G-A
• rs11660954
• NM_001375912.1:c.2528+1957G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF532	NM_001375912.1	MANE Select	c.2528+1957G>A		intron	N/A	NP_001362841.1
	ZNF532	NM_001318726.2		c.2528+1957G>A		intron	N/A	NP_001305655.1
	ZNF532	NM_001318727.2		c.2528+1957G>A		intron	N/A	NP_001305656.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF532	ENST00000591808.6	TSL:1 MANE Select	c.2528+1957G>A		intron	N/A	ENSP00000468238.1
	ZNF532	ENST00000336078.8	TSL:1	c.2528+1957G>A		intron	N/A	ENSP00000338217.4
	ZNF532	ENST00000591083.5	TSL:1	c.2528+1957G>A		intron	N/A	ENSP00000468532.1

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

African (AFR) AF: 0.0718 AC: 2978 AN: 41504

American (AMR) AF: 0.194 AC: 2968 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3470

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5188

South Asian (SAS) AF: 0.213 AC: 1024 AN: 4814

European-Finnish (FIN) AF: 0.357 AC: 3768 AN: 10550

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20489 AN: 67974

Other (OTH) AF: 0.241 AC: 508 AN: 2112

Alfa AF: 0.257 Hom.: 749

Bravo AF: 0.203

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.84
DANN	Benign	0.67
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11660954; hg19: chr18-56603803;