NM_001375912.1:c.3412-268C>G

Variant names:

• chr18-58983704-C-G
• rs17695069
• NM_001375912.1:c.3412-268C>G

Variant summary

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

The NM_001375912.1(ZNF532):​c.3412-268C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 151,404 control chromosomes in the GnomAD database, including 553 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 0.076 (553 hom., cov: 31)
• Consequence: ZNF532 NM_001375912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 2 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]

ENSG00000294809 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 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.3412-268C>G		intron	N/A	NP_001362841.1
	ZNF532	NM_001318726.2		c.3412-268C>G		intron	N/A	NP_001305655.1
	ZNF532	NM_001318727.2		c.3412-268C>G		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.3412-268C>G		intron	N/A	ENSP00000468238.1
	ZNF532	ENST00000336078.8	TSL:1	c.3412-268C>G		intron	N/A	ENSP00000338217.4
	ZNF532	ENST00000591083.5	TSL:1	c.3412-268C>G		intron	N/A	ENSP00000468532.1

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11534 AN: 151286 Hom.: 550 Cov.: 31

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.0760

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0257

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0581

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

GnomAD4 genome AF: 0.0762 AC: 11541 AN: 151404 Hom.: 553 Cov.: 31 AF XY: 0.0769 AC XY: 5685 AN XY: 73920

African (AFR) AF: 0.0193 AC: 795 AN: 41176

American (AMR) AF: 0.115 AC: 1750 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3470

East Asian (EAS) AF: 0.0258 AC: 130 AN: 5038

South Asian (SAS) AF: 0.0674 AC: 321 AN: 4766

European-Finnish (FIN) AF: 0.119 AC: 1247 AN: 10522

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6895 AN: 67948

Other (OTH) AF: 0.0575 AC: 121 AN: 2106

Alfa AF: 0.0414 Hom.: 35

Bravo AF: 0.0734

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.40
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17695069; hg19: chr18-56650936;