NM_001375912.1:c.2528+856T>A

Variant names:

• chr18-58935470-T-A
• rs73439953
• NM_001375912.1:c.2528+856T>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001375912.1(ZNF532):​c.2528+856T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 5)
• Consequence: ZNF532 NM_001375912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• 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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF532	NM_001375912.1	MANE Select	c.2528+856T>A		intron	N/A	NP_001362841.1	Q9HCE3
	ZNF532	NM_001318726.2		c.2528+856T>A		intron	N/A	NP_001305655.1	Q9HCE3
	ZNF532	NM_001318727.2		c.2528+856T>A		intron	N/A	NP_001305656.1	Q9HCE3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF532	ENST00000591808.6	TSL:1 MANE Select	c.2528+856T>A		intron	N/A	ENSP00000468238.1	Q9HCE3
	ZNF532	ENST00000336078.8	TSL:1	c.2528+856T>A		intron	N/A	ENSP00000338217.4	Q9HCE3
	ZNF532	ENST00000591083.5	TSL:1	c.2528+856T>A		intron	N/A	ENSP00000468532.1	Q9HCE3

Frequencies

GnomAD3 genomes Cov.: 5

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

GnomAD4 genome Cov.: 5

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-1.4

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: rs73439953; hg19: chr18-56602702;