18-58900674-G-T

Variant names:

• chr18-58900674-G-T
• rs937815
• NM_001375912.1:c.-17-17597G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375912.1(ZNF532):​c.-17-17597G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 152,138 control chromosomes in the GnomAD database, including 590 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 0.078 (590 hom., cov: 32)
• Consequence: ZNF532 NM_001375912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.12 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.-17-17597G>T		intron	N/A	NP_001362841.1
	ZNF532	NM_001318726.2		c.-17-17597G>T		intron	N/A	NP_001305655.1
	ZNF532	NM_001318727.2		c.-17-17597G>T		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.-17-17597G>T		intron	N/A	ENSP00000468238.1
	ZNF532	ENST00000336078.8	TSL:1	c.-17-17597G>T		intron	N/A	ENSP00000338217.4
	ZNF532	ENST00000591083.5	TSL:1	c.-17-17597G>T		intron	N/A	ENSP00000468532.1

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11898 AN: 152020 Hom.: 587 Cov.: 32

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0783 AC: 11905 AN: 152138 Hom.: 590 Cov.: 32 AF XY: 0.0783 AC XY: 5826 AN XY: 74374

African (AFR) AF: 0.0225 AC: 933 AN: 41518

American (AMR) AF: 0.124 AC: 1902 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 224 AN: 3472

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5172

South Asian (SAS) AF: 0.0663 AC: 319 AN: 4814

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10574

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7092 AN: 68000

Other (OTH) AF: 0.0632 AC: 133 AN: 2104

Alfa AF: 0.0895 Hom.: 585

Bravo AF: 0.0774

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		-0.027
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: rs937815; hg19: chr18-56567906;