18-58865588-C-T

Variant names:

• chr18-58865588-C-T
• rs7226876
• NM_001375912.1:c.-18+9C>T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF532	NM_001375912.1	c.-18+9C>T		intron_variant	Intron 2 of 9	ENST00000591808.6	NP_001362841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF532	ENST00000591808.6	c.-18+9C>T		intron_variant	Intron 2 of 9	1	NM_001375912.1	ENSP00000468238.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41830 AN: 151854 Hom.: 5970 Cov.: 32

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.: 43 Cov.: 0 AF XY: 0.258 AC XY: 122 AN XY: 472

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.284

Gnomad4 NFE exome AF: 0.268

Gnomad4 OTH exome AF: 0.239

GnomAD4 genome AF: 0.275 AC: 41853 AN: 151972 Hom.: 5973 Cov.: 32 AF XY: 0.275 AC XY: 20450 AN XY: 74260

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.282

Alfa AF: 0.255 Hom.: 6977

Bravo AF: 0.276

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.81

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: rs7226876; hg19: chr18-56532820;